专利摘要:
The present disclosure provides novel polypeptides having 3-buten-2-ol dehydratase activity, polypeptides having catalytic activity in the conversion of 3-methyl-3-buten-2-ol to isoprene, and crystal structure data. for one of these polypeptides. Methods of making and using the polypeptides and their related crystal structure data are also provided.
公开号:FR3033172A1
申请号:FR1651674
申请日:2016-02-29
公开日:2016-09-02
发明作者:Adriana Botes；Nadia Kadi；Mihai Luchian Azoitei；Yih-En A Ban；Daniela Grabs-Rothlisberger；Alexander Pisarchik；Alexandre Zanghellini；Eric Althoff
申请人:Invista North America LLC；
IPC主号:

专利说明:

[0001] MUTANT POLYPEPTIDES AND THEIR USES CROSS REFERENCE TO RELATED APPLICATIONS [1] The present application claims the benefit of U.S. Provisional Application No. 62/126279, filed February 27, 2015, the contents of which are hereby incorporated by reference in its entirety. SEQUENCE LIST [2] This application contains a sequence listing that has been filed electronically in ASCII format and is hereby incorporated by reference in its entirety. The ASCII copy, created on July 15, 2015, is named 12444.0235-00 SL.txt and its size is 1,439,337 bytes. FIELD [3] The present disclosure provides novel polypeptides having catalytic activity in the conversion of 3-buten-2-ol to butadiene, polypeptides having catalytic activity in the conversion of 3-methyl-3-buten-2-ol. isoprene, and crystal structure data for one of these polypeptides. Methods for producing and using the polypeptides and their related crystal structure data are also provided. BACKGROUND [004] 1,3-Butadiene (hereinafter referred to as butadiene) is an important monomer for the production of synthetic rubbers including styrene-butadiene rubber (SBR), polybutadiene (PB), styrene-butadiene latex (SBL), acrylonitrile-butadiene-styrene (ABS) resins, nitrile-based rubber, and adiponitrile, which is used in the manufacture of nylon-66 (White, Chemico-Biological Interactions, 2007, 166 , 10-14). Butadiene is usually produced as a co-product of the steam cracking process, distilled into a crude butadiene stream and purified by extractive distillation (White, Chemico-Biological Interactions, 2007, 166, 10-14). On an industrial scale, 95% of the world production of butadiene is carried out via the steam cracking process using petrochemical raw materials such as naphtha. Butadiene has also been prepared, among other processes, by the dehydrogenation of n-butane and n-butene (Houdry process) and the oxidative dehydrogenation of n-butene (process 0x0-D or O-XD) (White, Chemico -Biological Interactions, 2007, 166, 10-14). These processes are associated with high production costs and low yields (White, Chemico-Biological Interactions, 2007, 166, 10-14). [005] Isoprene is an important monomer for the production of special elastomers including engine mountings / mounts, surgical gloves, elastic tapes, golf balls and shoes. Styrene-isoprene block copolymers form an essential component of hot melt pressure sensitive adhesive formulations and cis-poly-isoprene is used in tire manufacturing (Whited et al., Industrial Biotechnology, 2010, 6 (3) 152-163). Manufacturers of rubber products depend on either imported natural rubber from Brazilian rubberwood or synthetic rubber-based synthetic polymers (Whited et al., 2010, supra). [006] Given the dependence on petrochemical raw materials and the catalytic stages that consume a lot of energy, biotechnology offers an alternative approach to the synthesis of butadiene and isoprene via biocatalysis. Biocatalysis is the use of biological catalysts, such as enzymes, to perform biochemical transformations of organic compounds. Accordingly, there is a need for sustainable methods of producing butadiene and isoprene, said methods being based on biocatalysis (Jang et al., Biotechnology & Bioengineering, 2012, 109 (10), 2437-2459). Raw materials of biological origin and those of petrochemical origin are acceptable starting materials for biocatalysis processes. SUMMARY [007] The present disclosure provides novel recombinant polypeptides that can catalyze the dehydration of 3-buten-2-ol to 1,3-butadiene and 3-methyl-3-buten-2-ol to isoprene. These novel polypeptides have many industrial applications in the biosynthesis of polymers. To improve their catalytic activity, one of these polypeptides has been crystallized and the respective crystal structure data is presented here. These crystal structure data can be used for modeling new, artificially created, improved enzymes with desired LDH activity. [8] Linalol dehydratase (EC 4.2.1.127, LDH) is a unique bifunctional enzyme that naturally catalyzes the dehydration of linalool to myrcene and the isomerization of linalool to geraniol. LDH can also catalyze the conversion of 3-methyl-3-buten-2-ol to isoprene. See PCT / US2013 / 045430, published as W0 / 2013/188546 and US Patent Publication No. 20150037860 incorporated herein by reference in their entirety. Isoprene can also be synthesized by other methods. See US Patent Publications Nos. 20150037860 and 20130217081, incorporated herein by reference in their entirety. [9] It has been discovered that Castellaniella defragrans LDH (cdLD) can also convert 3-buten-2-ol to 1,3-butadiene, albeit in low yields. New polypeptides having advantageous properties in the industrial synthesis of 1,3-butadiene are provided herein, as compared to those of the wild-type cdLD. These polypeptides have superior 3-buten-2-ol dehydratase activity and also superior activity in catalyzing the conversion of 3-methyl-3-buten-2-ol to isoprene. [10] The present description also shows the crystalline structure of apo cdLD, demonstrated by X-ray crystallography. Purified apo cdLD crystals were obtained and the three-dimensional structure of this enzyme was elucidated for the first time and independently confirmed. The elucidation of these crystal structure data allows a better understanding of the enzymatic activity of the cdLD and the intelligent design of many enhancements of it, as well as the development of various substrates and inhibitors. [11] Certain embodiments provide a polypeptide comprising an amino acid sequence having an amino acid sequence homology of at least 90% with SEQ ID NO: 1, wherein said amino acid sequence comprises at least at least one, preferably one to five, mutations at the following X-positions of SEQ ID NO: 1 R1_95X96R97-98X99R100-122X123R124-186X187R188-203X204R205-211X212R213- 272X273X274X275R276-323X324R325-327X328R329-R359X360R361-365X366R367- 381X382R383-398, wherein: 3 X98 is mutated to a different amino acid selected from L and equivalent amino acids; X99 is mutated to a different amino acid selected from L and equivalent amino acids; X123 is mutated to a different amino acid selected from I and equivalent amino acids; X187 is mutated to a different amino acid selected from M and equivalent amino acids; X204 is mutated to a different amino acid selected from I and equivalent amino acids; X212 is mutated to a different amino acid selected from F, Y, and equivalent amino acids; X273 is mutated to a different amino acid selected from C and equivalent amino acids; X274 is mutated to a different amino acid selected from F and equivalent amino acids; X275 is mutated to a different amino acid selected from I and equivalent amino acids; X324 is mutated to a different amino acid selected from L, E, and equivalent amino acids; X328 is mutated to a different amino acid selected from V and equivalent amino acids; X380 is mutated to a different amino acid selected from Y and equivalent amino acids; X388 is mutated to a different amino acid selected from V, C, G, and equivalent amino acids; X382 is mutated to a different amino acid selected from W and equivalent amino acids; and each R is identical to the corresponding amino acid in SEQ ID NO: 1. In another embodiment, the homology with SEQ ID NO: 1 is at least 91, at least 92, from minus 93, at least 94, at least 95, at least 96, at least 97, at least 98 or at least 99%. [012] In another embodiment, the polypeptide of the preceding paragraph is such that said amino acid sequence has an amino acid sequence homology of at least 91% with SEQ ID NO: 1, preferably a amino acid sequence homology of at least 92% with SEQ ID NO: 1, preferably amino acid sequence homology of at least 93% with SEQ ID NO: 1, preferably a sequence homology of amino acids of at least 94% with SEQ ID NO: 1, preferably at least 95% amino acid sequence homology with SEQ ID NO; preferably amino acid sequence homology of at least 96% with SEQ ID NO: 1, preferably amino acid sequence homology of at least 97% with SEQ ID NO: 1, preferably homology amino acid sequence of at least 98% with SEQ ID NO: 1, or preferably amino acid sequence homology of at least 99% with SEQ ID NO: 1. [013] Another mode Embodiment provides the polypeptide according to the preceding two paragraphs, wherein said amino acid sequence comprises one of the mutations specified at one of the following specified positions of SEQ ID NO: 1 Ri _95X98R97-98X99R100-122X123R124-186X187R188- Wherein X98 is mutated to a different amino acid selected from L and equivalent amino acids - X99 is mutated to a different amino acid selected from the group consisting of: ## STR00002 ## L and amino acids equiv Alents X123 is mutated to a different amino acid selected from I and equivalent amino acids X187 is mutated to a different amino acid selected from M and equivalent amino acids X204 is mutated to a different amino acid selected from I and equivalent amino acids X212 is mutated to a different amino acid selected from F, Y, and equivalent amino acids X273 is mutated to a different amino acid selected from C and equivalent amino acids X274 is mutated to a different amino acid selected from F and acids equivalent amino acids X275 is mutated to a different amino acid selected from I and equivalent amino acids; X324 is mutated to a different amino acid selected from L, E, and equivalent amino acids; X328 is mutated to a different amino acid selected from V and equivalent amino acids; X360 is mutated to a different amino acid selected from Y and equivalent amino acids; X366 is mutated to a different amino acid selected from V, C, G, and equivalent amino acids; X382 is mutated to a different amino acid selected from W and equivalent amino acids; and each R is identical to the corresponding amino acid in SEQ ID NO: 1 These enumerated positions are hereinafter referred to as the specified positions and these listed mutations are hereinafter referred to as the mutations specified. [014] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that said amino acid sequence comprises two mutations specified at two of the specified positions. [015] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that said amino acid sequence comprises three of the specified mutations at three of the specified positions. [16] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that said amino acid sequence comprises four of the mutations specified at four of the specified positions. [17] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that said amino acid sequence comprises five of the mutations specified at five of the specified positions. [18] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X96 is mutated to a different amino acid selected from L and equivalent amino acids. [19] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X99 is mutated to a different amino acid selected from L and equivalent amino acids. [20] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X123 is mutated to a different amino acid selected from I and equivalent amino acids. [21] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X187 is mutated to a different amino acid selected from M and equivalent amino acids. [22] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X204 is mutated to a different amino acid selected from I and equivalent amino acids. [023] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X212 is mutated to a different amino acid selected from F, Y, and equivalent amino acids. [24] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X273 is mutated to a different amino acid selected from among the equivalent amino acids. [25] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X274 is mutated to a different amino acid selected from F and equivalent amino acids. [26] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X275 is mutated to a different amino acid selected from I and equivalent amino acids. [27] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X324 is mutated to a different amino acid selected from L, E, and equivalent amino acids. [028] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X328 is mutated to a different amino acid selected from V and equivalent amino acids. [29] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X360 is mutated to a different amino acid selected from Y and equivalent amino acids. [30] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X366 is mutated to a different amino acid selected from V, C, G, and equivalent amino acids. [31] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that X382 is mutated to a different amino acid selected from W and equivalent amino acids. [32] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following four mutations: V1231, V2041, M274F and V2751; preferably, it comprises only these four mutations. [33] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following five mutations: V1231, V2041, M274F, V2751 and F382W; preferably, it comprises only these five mutations. [34] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: V2751 and F382W; preferably, it comprises only these two mutations. [035] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following four mutations: A324L, V2751, V1231 and V2041; preferably, it comprises only these four mutations. [36] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: A324L and S366G; preferably, it comprises only these two mutations. [37] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: M274F and F96L; preferably, it comprises only these two mutations. [038] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: M274F and Y99L; preferably, it comprises only these two mutations. [39] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: F382W and L212Y; preferably, it comprises only these two mutations. [40] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: F382W and A273C. [41] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: F382W and L328V; preferably, it comprises only these two mutations. [42] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: F382W, L328V and 1187M; preferably, it comprises only these three mutations. [43] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following three mutations: V2041, M274F and V275I; preferably, it comprises only these three mutations. [44] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following three mutations: V1231, M274F and V275I; preferably, it comprises only these three mutations. [45] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following three mutations: V1231, V2041 and V275I; preferably, it comprises only these three mutations. [046] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following three mutations: V1231, V2041 and M274F; preferably, it comprises only these three mutations. [47] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following three mutations: M274F, V275I and A324L; preferably, it comprises only these three mutations. [48] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following three mutations: M274F, V275I and F382W; preferably, it comprises only these three mutations. [49] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following four mutations: M274F, V275I, R360Y and F382W. [50] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: V275I and A324L; preferably, it comprises only these two mutations. [51] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises the following two mutations: R360Y and F382W; preferably, it comprises only these two mutations. [52] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it comprises a C-terminal His (tag-tag). [053] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that it lacks a periplasmic label. [054] In another embodiment, the polypeptide according to the preceding paragraphs of this SUMMARY is such that the polypeptide has activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or or in catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene which is at least 80% of that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8 , increased by a factor of about 1.5 or more relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor 2 or greater with respect to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor of 2.5 relative to that of a polypeptide consisting of SEQ ID NO: 1, 4 , 5, 7 or 8, preferably by a factor of about 3 or more, relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7, or 8, preferably a factor of 3, 5 approximately 25 or more by to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 4 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably by a factor of about 4.5 or higher relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8 or preferably about a factor of 5 or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, and wherein said activity is observed in at least one activity assay. In another embodiment, said specific activity is measured with a purified protein and is observed in at least one specific activity assay. In another embodiment, said activity in catalyzing the dehydration of 3-buten-2-ol to 10, 3-butadiene and / or in catalyzing the dehydration of 3-methyl-3-buten-2-ol isoprene is observed in at least one type of non-bacterial cell. In another embodiment, said activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in catalyzing the dehydration of 3-methyl-3-buten-2-ol isoprene is observed in at least one type of bacteria. In another embodiment, said activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in catalyzing the dehydration of 3-methyl-3-buten-2-ol isoprene is observed in more than one type of bacteria. In another embodiment, the bacteria are a strain of E. Coll. In another embodiment, the bacteria are Origami2 (DE3) or BL21 (DE3). [055] Embodiments for a derivative of any of the polypeptides according to the preceding paragraphs of this SUMMARY are also provided. [056] Embodiments for a polynucleotide comprising, consisting of or consisting essentially of a nucleic acid encoding any of the polypeptides or derivatives according to the preceding paragraphs of this SUMMARY, preferably with codon optimization, are also provided. . In another embodiment, the polynucleotide is a DNA molecule or an RNA molecule. In another embodiment, the polynucleotide further comprises a promoter operably linked to the nucleic acid sequence encoding the polypeptide or derivative. [57] Embodiments for a recombinant expression vector comprising a DNA molecule as described in any one of the preceding nucleotide paragraphs are also provided. [58] Embodiments for a host cell that is transformed or transduced with a DNA molecule as described in any of the preceding paragraphs relating to a nucleotide or a recombinant expression vector according to the preceding paragraph are also provided.
[0002] In another embodiment, the cell is such that the DNA molecule or recombinant expression vector is integrated into a chromosome of the cell.  [59] Embodiments for an organism, preferably a microorganism, comprising a heterologous DNA molecule encoding a polypeptide according to any one of the preceding paragraphs relating to a polypeptide of this SUMMARY are also provided.  In another embodiment, the microorganism is a bacterium or a fungus.  In another embodiment, the microorganism is an E bacterium.  Coli or a bacterium Castellaniella defragrans.  Embodiments for a transgenic animal or plant comprising a heterologous DNA molecule encoding a polypeptide according to any one of the preceding paragraphs relating to a polypeptide of this SUMMARY are also provided.  [61] Embodiments for a vector comprising a DNA molecule according to any one of the preceding paragraphs relating to a DNA molecule of this SUMMARY are also provided.  [62] Certain embodiments provide a method of producing a polypeptide according to any one of the preceding paragraphs relating to a polypeptide of this SUMMARY, the method comprising: (i) preparing an expression construct which comprises a polynucleotide according to any one of the preceding paragraphs relating to a polynucleotide of this SUMMARY, with a sequence coding for the polypeptide according to any one of the preceding paragraphs relating to a polypeptide of the present SUMMARY, operably linked to one or more regulatory nucleotide sequences; (ii) transfection or transformation of an appropriate host cell with the expression construct; (iii) expressing the recombinant polypeptide in said host cell; and (iv) isolating or purifying the recombinant polypeptide from said host cell or using the host cell obtained as such or as a cell extract.  [63] Another embodiment provides a method of making a polypeptide having an activity of at least 80% or improved activity, in catalyzing the dehydration of 3-buten-2-ol by butadiene and / or in catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, the method comprising the preparation of a polypeptide according to any one of the polypeptide paragraphs of this SUMMARY.  [064] Also provided as embodiments are compositions comprising one or more polypeptides according to any one of the preceding paragraphs of this SUMMARY.  In another embodiment, the composition further comprises the polypeptide of SEQ ID NO: 1, 4, 5, 7 or 8.  In another embodiment, any one of these compositions comprises one or more, preferably more than one, in certain embodiments, polypeptides according to any one of the present polypeptide-related polypeptide at least 80% or increased activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in catalyzing the dehydration of 3-methyl-3-buten-2- ol isoprene, relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8.  In some of these embodiments, the reference polypeptide is devoid of a periplasmic label.  In some of these embodiments, the reference polypeptide has a His tag.  In some of these embodiments, the reference polypeptide is devoid of a periplasmic tag and has a His tag.  Embodiments for these compositions further comprising 3-buten-2-ol and / or 3-methyl-3-buten-2-ol are also provided.  In other embodiments, these compositions further include 1,3-butadiene and / or isoprene.  [065] In another embodiment there is also provided a composition which comprises a rubber product, polymerized from 1,3-butadiene produced in the presence of a polypeptide according to any one of present ABSTRACT.  In one embodiment there is also provided a composition which comprises (additionally) a rubber product, polymerized from isoprene produced in the presence of a polypeptide according to any one of the polypeptide paragraphs of this SUMMARY.  [066] In another embodiment there is also provided a composition comprising a copolymer polymerized from 1,3-butadiene produced in the presence of a polypeptide according to any one of the polypeptide paragraphs of this SUMMARY.  In a related embodiment there is also provided a composition which comprises (additionally) a copolymer product polymerized from isoprene produced in the presence of a polypeptide 13 according to any one of the polypeptide paragraphs of this SUMMARY.  [67] In another embodiment there is also provided a composition comprising a plastic product polymerized from 1,3-butadiene produced in the presence of a polypeptide according to any of the polypeptide-related paragraphs herein. ABSTRACT.  In this embodiment there is also provided a composition which comprises (additionally) a plastic product polymerized from isoprene produced in the presence of a polypeptide according to any one of the polypeptide paragraphs of this SUMMARY.  [68] In another embodiment is also provided an antibody capable of binding to a polypeptide according to any one of the polypeptide paragraphs of this SUMMARY.  [69] Another embodiment provides a fusion protein comprising a polypeptide according to any one of the polypeptide paragraphs of this SUMMARY.  [70] Another embodiment provides a complex comprising a polypeptide according to any one of the polypeptide paragraphs of this SUMMARY, and said complex optionally further comprising 3-buten-2-ol.  Another embodiment provides a complex comprising a polypeptide according to any of the polypeptide paragraphs of this SUMMARY, said complex further comprising optionally 3-methyl-3-buten-2-ol.  Another embodiment provides a composition comprising 3-buten-2-ol and a means for producing 1,3-butadiene.  [72] Another embodiment provides a composition comprising a substrate and a means for enzymatically producing 1,3-butadiene from said substrate.  [73] Another embodiment provides a process for producing 1,330 butadiene comprising: a step of enzymatically converting 3-buten-2-ol to 1,3-butadiene; and measuring and / or harvesting the 1,3-butadiene thus produced.  [74] Another embodiment provides a container and means for producing 1,3-butadiene.  [75] Another embodiment provides a method of designing a polypeptide having at least 80% activity or increased activity in catalyzing the dehydration of 3-buten-2-ol by butadiene relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, the process comprising the mutation of a 3-buten-2-ol enzymatic conversion means to butadiene.  [76] Another embodiment provides a composition comprising 3-methyl-3-buten-2-ol and a means of producing isoprene.  [77] Another embodiment provides a composition comprising a substrate and isoprene enzymatic production means from said substrate.  [78] Another embodiment provides a process for producing isoprene comprising: a step of enzymatically converting 3-methyl-3-buten-2-ol to isoprene; and measuring and / or harvesting the isoprene thus produced.  [79] Another embodiment provides a container and means for producing isoprene.  [80] Another embodiment provides a method of designing a polypeptide having an activity of at least 80% or increased activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol by isoprene compared to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, the process comprising the mutation of an enzymatic conversion means of 3-methyl-3-buten-2-ol into isoprene.  [081] Another embodiment provides a crystal having the coordinates shown in Appendix I in space group P2 (1) with cellular parameters a = 133.18 A, b = 110.83 A, c = 162, A, which is produced from a polypeptide consisting of the amino acid sequence of SEQ ID NO: 5 with up to 2% variation in any cell size.  In another embodiment, it is provided that the same crystal is produced from a polypeptide consisting of the amino acid sequence of SEQ ID NO: 8 (SEQ ID NO: 5 without His tag).  [082] Another embodiment provides a crystal having the coordinates shown in Appendix I in space group P2 (1) with cellular parameters a = 133.18 A, b = 110.83 A, c = 162.20 A, which is produced from a polypeptide consisting of the amino acid sequence of SEQ ID NO: 5.  In another embodiment, it is provided that the same crystal is produced from a polypeptide consisting of the amino acid sequence of SEQ ID NO: 8 (SEQ ID NO: 5 without His tag).  [083] Another embodiment provides a crystal according to the crystals described in the preceding paragraphs, which diffracts X-rays for determining the atomic coordinates of the crystal at a resolution between 48.16 A and 2.54 A.  [084] Another embodiment provides a crystal according to the crystals described in the preceding paragraph, which comprises an active site comprising one or more residues selected from those of the following table, labeled according to SEQ ID NO: 1 according to the coordinates of the Annex 1: Position Type of residue Chain 65 ASP C 66 PHE C 71 TYR C 89 VAL A 91 LYS A 92 TYR A 96 PHE A 151 MET A 155 HAS A 197 CYS A 198 GLU A 203 PHE A 205 GLN A 206 CYS A 209 VAL A 266 TYR A 267 THR A 270 TRP A 319 VAL A 321 LEU A 325 PHE A 367 LEU A 368 LEU A 372 LEU A [085] Another embodiment provides a crystal according to any one of the crystals described in the preceding paragraphs, which comprises a disulfide bridge between Cys74 and Cys127 residues of a polypeptide of SEQ ID NO: 5.  Another embodiment provides a crystal according to any one of the crystals described in the preceding paragraphs, which comprises a disulfide bridge between Cys74 and Cys127 residues of a polypeptide of SEQ ID NO: 8, wherein the numbers residues are related to SEQ ID NO: 1.  [86] Another embodiment provides a co-crystal comprising the crystal 5 according to any one of the crystals described in the preceding paragraphs, bonded to a substrate such as linalool, 3-buten-2-ol or 3 -méthy1-3-buten-2-ol.  [87] Another embodiment provides a method for identifying a LDH substrate or inhibitor, comprising any one or more of the following steps: (a) obtaining a crystal or coordinates of a crystal, a polypeptide comprising SEQ ID NO: 5 or 8, the crystal being in a P2 (1) cluster, with unit cell sizes of about a = 133.18 A, of about b = 110; , 83A, about c = 162.20A; (b) obtaining or determining the three-dimensional structure of said polypeptide using the crystal of point (a) by an X-ray diffraction method; (c) presenting the three-dimensional structure of said complex on a computer by inputting said crystal structure data of said polypeptide, the computer comprising software for generating said three-dimensional structure and for identifying a substrate or inhibitor; and (d) selecting a substrate or inhibitor of the active site of said polypeptide.  In certain related embodiments, the substrate is selected from linalool, 3-buten-2-ol and 3-methyl-3-buten-2-ol.  [88] Another embodiment provides a method for designing a LDH substrate or inhibitor, the method comprising any one or more of the following steps: (a) obtaining a crystal or co-ordinates of a crystal, in a P2 (1) space group with the cellular parameters a = 133.18 A, b = 110.83 A, c = 162.20 A, of a complex consisting of a SEQ ID polypeptide NO: 5 or 8 bound to a substrate or inhibitor at its binding site; (b) obtaining or determining the three-dimensional structure of the complex by using the crystal obtained in point (a) by an X-ray diffraction method to obtain the atomic coordinates of the structure; (c) providing on a computer the atomic coordinates of the three-dimensional structure of the complex; and (d) using a program run by the computer to design a chemical compound predicted to bind to the polypeptide of SEQ ID NOs: 5 or 8 at the substrate or inhibitor binding site and acting as a substrate or LDH inhibitor, based on said three-dimensional structure.  In a related embodiment, the design includes the de novo rational design of a drug and / or the computer design of a protein.  In a related embodiment, the design includes the use of docking software and screening of one or more databases of molecules that adapt to the substrate binding site on the polypeptide of SEQ ID NO: 5 or 8.  In certain related embodiments, the substrate is selected from linalool, 3-buten-2-ol and 3-methyl-3-buten-2-ol.  In certain related embodiments, the rational drug design and / or computer design of a protein is based on interactions between one or more residues of the predicted active site of the polypeptide of SEQ ID NO: 5 or 8 and the linalool, 3-buten-2-ol or 3-methyl-3-buten-2-ol.  In some embodiments, one or more of the following residues (numbered in connection with SEQ ID NO: 1) are part of the active site: Position Type of residue String 65 ASP C 66 PHE C 71 TYR C 89 VAL A 91 LYS A 92 TYR A 96 PHE A 151 MET A 155 HIS A 197 CYS A 198 GLU A 203 PHE A 205 GLN A 206 CYS A 209 VAL A 266 TYR A 267 THR A 270 TRP A 319 VAL A 321 LEU A 325 PHE A 367 LEU A Another embodiment provides a method according to any one of the methods described in the preceding methods related to the crystal, further comprising one or more of: (e) synthesis or obtaining the compound; and (f) evaluating the compound to determine its ability to perform one or more of (1) polypeptide binding of SEQ ID NO: 5 or 8, (2) competition with linalool, 3-butene, and 2-ol or 3-methyl-3-buten-2-ol for binding of the polypeptide of SEQ ID NO: 5 or 8, (3) inhibition of LDH, or (4) dehydration by the polypeptide of SEQ ID NO: 5 or 8.  [90] Another embodiment provides a process for preparing the crystal of the polypeptide of SEQ ID NO: 5 or 8 according to any one of the preceding paragraphs, which comprises: (a) providing a solution having said polypeptide, in a suitable buffer such as Tris buffer pH about 8 to about 20 mM, NaCl about 150 mM, glycerol about 5%; (b) mixing the solution with a crystallization solution comprising about 10% P8000, about 20% ethylene glycol, about 0.02 M Na-1-glutamate, dl-alanine at about 0.02M, glycine at about 0.02M, dl-lysine HCl at about 0.02M, dl-serine at about 0.02M; and (c) incubating the mixture under conditions and for a time sufficient to promote crystal production of the polypeptide of SEQ ID NO: 5 or 8.  [91] Another embodiment provides a method for preparing the cocrystal according to the foregoing co-crystal-related paragraphs of this SUMMARY, which comprises the steps of: (a) providing a solution having said polypeptide, in an appropriate buffer such as Tris buffer of about pH 8 to about 20 mM, about 150 mM NaCl, about 5% glycerol; (b) mixing the solution with a crystallization solution comprising about 10% P8000, about 20% ethylene glycol, and about 0.02 M Na-1-glutamate. from about 0.02M dl-alanine, about 0.02M glycine, about 0.02M dl-lysine HCl, about 0.02M dl-serine; and (c) incubating the mixture under conditions and for a time sufficient to produce the co-crystal of the polypeptide bound to said substrate, such as linalool, 3-buten-2-ol or 3-methyl-3-butenediol. 2-ol.  Another embodiment provides a method of identifying a compound that binds to the polypeptide of SEQ ID NO: 5 or 8, comprising: (a) obtaining a crystal comprising a protein consisting of SEQ ID NO: 5 or 8, in a P2 (1) space group with cellular parameters a = 133.18 A, b = 110.83A, c = 162.20A; (b) determining the three-dimensional structure of said polypeptide by X-ray diffraction to obtain the atomic coordinates of Appendix I; (c) contacting the structure of the polypeptide defined by the atomic coordinates of Appendix I or a subgroup thereof with a test compound; and (d) detecting an interaction between the compound and the atomic coordinates, wherein an energy-favored interaction between the test compound and the atomic coordinates is indicative of a compound that binds to said polypeptide.  [93] Another embodiment provides a crystal as defined in any one of the preceding crystal-related paragraphs, wherein the atomic coordinates define one or more regions as indicated in Table 3.  [94] Another embodiment provides a polypeptide according to any one of the preceding paragraphs relating to the polypeptide of this SUMMARY, the polypeptide having activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol by isoprene which is at least 80% of that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, increased by a factor of about 1.5 or greater relative to that of a polypeptide consisting of SEQ ID NO: SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor 2 or greater relative to that of a polypeptide consisting of SEQ ID NO: SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 2.5 fold higher than that of a polypeptide consisting of SEQ ID NO: SEQ ID NO: 1, 4, 5, 7 or 8, preferably by a factor of about 3 or more relative to that of a polypeptide consisting of SEQ ID NO: SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor 3.5 or greater by ratio ort to that of a polypeptide consisting of SEQ ID NO: SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor 4 or greater relative to that of a polypeptide consisting of SEQ ID NO SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 4.5 fold or greater than that of a polypeptide consisting of SEQ ID NO: SEQ ID NO: 1, 4, 5 , 7 or 8, or preferably by a factor of about 5 or more with respect to that of a polypeptide consisting of SEQ ID NO: SEQ ID NO: 1, 4, 5, 7 or 8, or preferably a about 15 or greater than that of a polypeptide consisting of SEQ ID NO: 1.4, 5, 7 or 8, and wherein said activity is observed in at least one assay of activity or preferably one about 55 or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 30 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, and wherein said activity is observed in at least one activity assay.  In certain related embodiments, said activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene is observed in at least one type of non-bacterial cell.  In certain other related embodiments, said activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene is observed in at least one type of bacteria.  In certain other related embodiments, said activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene is observed in more than one type of bacteria.  In some related embodiments, the bacteria are a strain of E. coli.  Coll.  In some related embodiments, the bacteria are Origami2 (DE3) or BL21 (DE3).  [95] Another embodiment provides a composition comprising 3-methyl-3-buten-2-ol and a means for producing isoprene.  Another embodiment provides a composition comprising a substrate and means for enzymatically producing isoprene from said substrate.  [97] Another embodiment provides a process for producing isoprene comprising: a step of enzymatically converting 3-methyl-3-buten-2-ol to isoprene; and measuring and / or harvesting the isoprene thus produced.  [98] Another embodiment provides an apparatus comprising a container and means for producing isoprene.  [99] Another embodiment provides a method of designing a polypeptide having at least 80% activity or enhanced activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol by isoprene compared to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, the method comprising the mutation of a means for enzymatically converting 3-methyl-3-buten-2 -ol isoprene.  Another embodiment provides a polypeptide comprising any one or more of the sequences for each of the mutants identified in Appendix 3.  Another embodiment provides a polypeptide comprising any one or more of the sequences for each of the mutants identified in Table 9.  Another embodiment provides a method of producing an enzyme which has improved activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in the catalysis of the converting 3-methyl-3-buten-2-ol to isoprene comprising: identifying reactive amino acid functional groups and functional group geometry to catalyze said reaction, thereby building an active site; constructing a set of amino acid rotamers from a structural library in which the rotamers incorporate said functional groups and said functional group geometry; the computer identification of an active site placement in a set of candidate protein backbones by a hashing algorithm, wherein the set of amino acid rotamers comprising said active site placement is positioned on a candidate protein backbone of so that the active site satisfies the stereochemistry of the protein and maintains a catalytic geometry; computer selection of an amino acid sequence to fit the identified skeleton and the placed active site, thereby identifying a hypothetical enzyme; the production of the hypothetical enzyme and the confirmation of the activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in catalyzing the conversion of 3-methyl-3-methyl- buten-2-ol in isoprene.  In one embodiment, this method is performed in accordance with one or more of the enzyme design techniques disclosed in US Patent No. 8,340,951.  Another embodiment provides a process for the production of isoprene, myrcene and / or 1,3-butadiene, comprising the cultivation or growth of a host cell or organism according to one of the following: any of the preceding paragraphs of this SUMMARY under conditions and for a period of time sufficient to produce isoprene, myrcene and / or 1,3-butadiene.  Another embodiment provides a culture medium comprising isoprene, myrcene and / or 1,3-butadiene, the said isoprene, myrcene and / or 1,3-butadiene biores having an isotopic ratio of carbon-12, carbon-13 and carbon-14, which reflects an absorption source of atmospheric carbon dioxide.  In some embodiments, said culture medium is separated from a host cell or organism according to any of the preceding paragraphs of this SUMMARY.  Another embodiment provides isoprene, myrcene, and / or 1,3-butadiene having an isotopic ratio of carbon-12, carbon-13 and carbon-14 which reflects an absorption source. atmospheric carbon dioxide, preferably produced by culturing a host cell or organism according to any of the preceding paragraphs of this summary.  In certain embodiments, said isoprene, myrcene, and / or 1,3-butadiene bioreseal of claim 115, said isoprene, myrcene, and / or 1,3-butadiene, having a Fm value of at least 80 ° / (:), at least 85 ° / (:), at least 90 ° / (:), at least 95% or at least 98%.  Certain embodiments provide a composition comprising said isoprene, myrcene, and / or 1,3-butadiene, bioderivated according to any one of the preceding paragraphs of this SUMMARY and a compound other than said isoprene, myrcene, and / or 1,3-butadiene. butadiene bioderected.  In certain embodiments of said compositions, said compound other than said isoprene, myrcene, and / or 1,3-butadiene is a trace amount of a cell part of a host cell or organism according to any one of paragraphs of this summary.  Some embodiments provide a biobased polymer comprising isoprene, myrcene and / or 1,3-butadiene bioriod according to any one of the preceding paragraphs of this SUMMARY.  Some embodiments provide a biobased resin comprising isoprene, myrcene and / or 1,3-butadiene bioriod according to any one of the preceding paragraphs of this SUMMARY.  Some embodiments provide a molded product obtained by molding a biobased polymer according to any one of the preceding paragraphs of this SUMMARY.  Some embodiments provide a method for producing a biobased polymer according to claim 119, comprising the chemical reaction of isoprene, myrcene and / or 1,3-butadiene, bio-derivative, according to any one of of the preceding paragraphs of this SUMMARY with itself or another compound in a reaction producing a polymer.  Some embodiments provide a molded product obtained by molding a biologically-based resin according to any one of the preceding paragraphs of this SUMMARY.  Certain embodiments provide a process for producing a biobased resin according to any one of the preceding paragraphs of this SUMMARY, comprising the chemical reaction of said isoprene, myrcene, and / or 1,3-butadiene with itself or another compound in a reaction producing a resin.  An embodiment provides a crystal comprising the coordinates indicated in Appendix 2 in the P2 (1) space group with the cellular parameters a = 88.7 A, b = 111.22 A, c = 120.42 To which is produced from a polypeptide consisting of the amino acid sequence of SEQ ID NO: 9 with a variation of up to 2% in a cell size.  An embodiment provides a composition comprising said crystal.  In some embodiments, said crystal diffracts X-rays for determining the atomic coordinates of the crystal at a resolution between 2.67A and 2.60A.  In embodiments, said crystal comprises a metal ion, preferably zinc.  Some embodiments provide a co-crystal comprising the crystal as defined in paragraph [0111] bound to a substrate such as linalool, 3-buten-2-ol and 3-methyl-3-buten. -2-ol.  Certain embodiments provide a method of identifying a LDH substrate or inhibitor, comprising any one or more of the following steps: (a) obtaining a crystal or coordinates of a crystal, of a polypeptide comprising SEQ ID NO: 8 or 9, the crystal being in a P2 (1) spatial group with the cellular parameters a = 88.7 A, b = 111.22 A, c = 120.42 A ; (b) obtaining or determining the three-dimensional structure of said polypeptide using the crystal of point (a) by an X-ray diffraction method; (c) displaying the three-dimensional structure of said complex on a computer by inputting said crystal structure data of said polypeptide, the computer comprising software for generating said three-dimensional structure and for identifying a substrate or inhibitor; and (d) selecting a substrate or inhibitor of the active site of said polypeptide.  Some embodiments provide a method for designing a LDH substrate or inhibitor, the method comprising one or more of the following steps: (a) obtaining a crystal or crystal coordinates in a P2 (1) spatial group, with cellular parameters a = 88.7 A, b = 111.22 A, c = 120.42 A of a complex consisting of a polypeptide of SEQ ID NO: 8 or 9 bound to the substrate or inhibitor at its binding site; (b) obtaining or determining the three-dimensional structure of the complex by using the crystal obtained in point (a) by an X-ray diffraction method to obtain the atomic coordinates of the structure; (c) providing on a computer the atomic coordinates of the three-dimensional structure of the complex; and (d) using a program run by the computer to design a chemical compound predicted to bind to the polypeptide of SEQ ID NO: 8 or 9 at the substrate binding site or inhibitor and acting as a substrate or LDH inhibitor, based on said three-dimensional structure.  In some embodiments of the method, the design includes the de novo rational design of a drug and / or the computer design of a protein.  In other embodiments of said method, the design comprises the use of a docking software and the screening of one or more databases of molecules that adapt to the binding site of the substrate on the Polypeptide of SEQ ID NO: 8 or 9.  Some embodiments provide a method according to paragraph [0114], further comprising any one or more of: (e) synthesizing or obtaining the compound; and (f) evaluating the compound for its ability to perform one or more of (1) binding of the polypeptide of SEQ ID NO: 8 or 9, (2) competition with linalool, 3-buten -2-ol or 3-methyl-3-buten-2-ol for binding of the polypeptide of SEQ ID NO: 8 or 9, (3) inhibition of LDH, or (4) dehydration by the polypeptide of SEQ ID NO: 8 or 9.  In certain embodiments, the method of [0114], wherein the rational design of a drug and / or the computer design of a protein is based on the interactions between one or more of the residues. (active predictive site) of the polypeptide of SEQ ID NO: 8 or 9 and linalool, 3-buten-2-ol or 3-methyl-3-buten-2-ol.  Certain embodiments provide a method for preparing the crystal of the polypeptide of SEQ ID NO: 8 or 9 according to paragraph [0111], which comprises: (a) providing a solution having said polypeptide, in a suitable buffer such as about 10 mM Tris (about pH 9.0), about 350 mM NaCl, and about 2 mM ditiothreitol, (b) mixing equal volumes of the solution with a crystallization solution comprising about 61 mM SS + + about 39 mM imidazole (about pH 6.5), about 13.2% (w / v) PEG 8000; about 26.4 ° A) (v / v) ethylene glycol; about 20 mM each of L-Naglutamate; alanine (racemic); glycine; lysine HCI (racemic); serine (racemic) and, optionally, about 0.05% (v / v) of 3-buten-2-ol; and (c) incubating the mixture under conditions and for a time sufficient to promote crystal production of the polypeptide of SEQ ID NO: 8.  Some embodiments provide a method for preparing the co-crystal according to paragraph [0112], which comprises the steps of: (a) providing a solution having said polypeptide, in a suitable buffer such as Tris at about 10 mM (about pH 9.0), about 350 mM NaCl, and about 2 mM ditothreitol; (b) mixing equal volumes of the solution with a crystallization solution comprising MES at about 61 mM + about 39 mM imidazole (about pH 6.5), about 13.2 ° A) (w / v) of PEG 8000; about 26.4 ° A) (v / v) ethylene glycol; about 20 mM each of L-Na-glutamate; alanine (racemic); glycine; lysine HCI (racemic); serine (racemic) and, optionally, 3-buten-2-ol at about 0.05% (v / v); and (c) incubating the mixture under conditions and for a time sufficient to promote the production of the cocrystal of said polypeptide bound to said substrate, such as linalool, 3-buten-2-ol or 3-methyl-3-one. buten-2-ol.  Some embodiments provide a method of identifying a compound that binds to the polypeptide of SEQ ID NO: 8 or 9, comprising: (a) obtaining a crystal comprising a protein consisting of SEQ ID NO: 9, the crystal being in a P2 (1) space group with cellular parameters a = 88.7 A, b = 111.22 A, c = 120.42 A; (b) determining the three-dimensional structure of said polypeptide by X-ray diffraction to obtain the atomic coordinates of Annex 2; (c) contacting the polypeptide structure defined by the atomic coordinates of Annex 2, or a subgroup thereof with a test compound; and (d) detecting an interaction between the compound and the atomic coordinates, an energy-favored interaction between the test compound and the atomic coordinates indicative of a compound that binds to said polypeptide.  Some embodiments provide the crystal according to paragraph [0111], the atomic coordinates defining one or more regions as indicated in Table 3.  Certain embodiments provide a crystal according to any one of paragraphs [0111] to [0121], wherein the crystal is obtained from a polypeptide comprising SEQ ID NO: 8.  Some embodiments provide a crystal comprising the coordinates of Appendix 1 or 2, preferably the crystal being prepared from a polypeptide comprising SEQ ID NO: 8.  Some embodiments provide a crystal having the same three-dimensional structure as any one of the three-dimensional structures represented by the coordinates of Appendix 1 or Appendix 2, preferably the crystal being prepared from a polypeptide comprising SEQ ID NO: 8.  Some embodiments provide a co-crystal comprising the crystal as defined in the substrate-bound paragraph [0124], such as linalool, 3-buten-2-ol and 3-methyl-3-methyl. buten-2-ol.  Some embodiments provide a method for identifying a LDH substrate or inhibitor, comprising any one or more of the following steps: (a) obtaining a crystal as described in paragraph [0124]; (b) obtaining or determining the three-dimensional structure of said polypeptide using the crystal of point (a) by an X-ray diffraction method; (c) displaying the three-dimensional structure of said complex on a computer by inputting said crystal structure data of said polypeptide, the computer comprising software for generating said three-dimensional structure and for identifying a substrate or inhibitor; and (d) selecting a substrate or inhibitor of the active site of said polypeptide.  Some embodiments provide a method of designing a LDH substrate or inhibitor, the method comprising any one or more of the following steps: (a) obtaining a crystal as described in [0124], a complex consisting of a polypeptide comprising SEQ ID NO: 8 bound to the substrate or an inhibitor at its binding site; (b) obtaining or determining the three-dimensional structure of the complex using the crystal obtained in paragraph (a) by an X-ray diffraction method to obtain the atomic coordinates of the structure; (c) providing on a computer, atomic coordinates of the three-dimensional structure of the complex; and (d) using a program run by the computer to design a chemical compound predicted to bind to the polypeptide of SEQ ID NO: 8 at the substrate or inhibitor binding site and acting as a substrate or inhibiting LDH, based on said three-dimensional structure.  Some embodiments provide a method according to paragraphs [0126] - [0127], wherein the design comprises the de novo rational design of a drug and / or the computer design of a protein.  Some embodiments provide a method according to paragraphs [0126] - [0127], wherein the design comprises the use of docking software and the screening of one or more databases of molecules that adapt to the substrate binding site on the polypeptide of SEQ ID NO: 8.  Some embodiments provide a method according to paragraphs [0126] - [0127], further comprising any one or more of: (e) synthesizing or obtaining the compound; and (f) evaluating the compound for its ability to achieve one or more of (1) binding of the polypeptide comprising SEQ ID NO: 8, (2) competition with linalool, 3-buten-2, and -ol or 3-methyl-3-buten-2-ol for binding of the polypeptide of SEQ ID NO: 8, (3) inhibition of LDH, or (4) dehydration by the polypeptide of SEQ ID NO [0131] Certain embodiments provide a method according to paragraph [0128], wherein the rational design of a drug and / or the computer design of a protein is based on the interactions between one or several of the residues (predictive active site) of the polypeptide of SEQ ID NO: 8 and linalool, 3-buten-2-ol or 3-methyl-3-buten-2-ol.  Some embodiments provide a method of preparing a crystal according to paragraph [0124], which comprises: (a) providing a solution having said polypeptide in an appropriate buffer such as Tris at about 20 mM about pH 8, NaCl about 150 mM, glycerol about 5%; (b) mixing the solution with a crystallization solution 28 comprising about 10% P8000; ethylene glycol at about 20%; about 0.02 M Na-1-glutamate, about 0.02 M dl-alanine, about 0.02 M glycine, about 0.02 M dl-lysine HCl, dl-serine about 0.02 M; or (a) providing a solution having said polypeptide, in a suitable buffer such as Tris at about 10 mM (about pH 9.0), about 350 mM NaCl, and about 2 mM iothreitol; (b) mixing equal volumes of the solution with a crystallization solution comprising MES at about 61 mM + about 39 mM imidazol (about pH 6.5), about 13.2% (w / v) PEG 8000 ; about 26.4% (v / v) ethylene glycol; about 20 mM each of L-Na-glutamate; alanine (racemic); glycine; lysine HCI (racemic); serine (racemic) and optionally, 3-buten-2-ol at about 0.05% (v / v); and (c) incubating the mixture under conditions and for a time sufficient to promote the production of the crystal according to paragraph [0124].  Some embodiments provide a method for preparing the co-crystal according to paragraph [0124], which comprises the steps of: (a) providing a solution having said polypeptide, in an appropriate buffer such as Tris at about About 20 mM pH 8, about 150 mM NaCl, about 5% glycerol; (b) mixing the solution with a crystallization solution comprising about 10% PEG 8000, about 20% ethylene glycol, about 0% Na-1-glutamate, 02 M, dl-alanine at about 0.02 M, glycine at about 0.02 M, dl-lysine HCl at about 0.02 M, dl-serine at about 0.02 M; and (c) incubating the mixture under conditions and for a time sufficient to promote the production of the co-crystal of said polypeptide bound to said substrate, such as linalool, 3-buten-2-ol or 3-methyl 3-buten-2-ol.  Some embodiments provide a method of identifying a compound that binds to a polypeptide comprising SEQ ID NO: 8, comprising: (a) obtaining a crystal according to paragraph [0124]; (b) determining the three-dimensional structure of said polypeptide by X-ray diffraction to obtain the atomic coordinates of Annex 1 or 2; (c) contacting the polypeptide structure defined by the atomic coordinates of Annex 1 or 2, or a subgroup thereof with a test compound; and (d) detecting an interaction between the compound and the atomic coordinates, an energy-favored interaction between the test compound and the atomic coordinates indicative of a compound that binds to said polypeptide.  Some embodiments provide a method of improving one or more of the catalytic activities of an LDH or fragment thereof, the method comprising one or more of the following steps: (a) obtaining a crystal as described in any one of the preceding paragraphs; (b) obtaining or determining the three-dimensional structure of the LDH by using the crystal obtained in (a) optionally by an X-ray diffraction method to obtain the atomic coordinates of the structure; (C) providing a computer with the atomic coordinates of the three-dimensional structure of the complex; and (d) using a computer design or software executed by the computer to design an LDH or fragment thereof, having one or more enhanced catalytic activities, based on said three-dimensional structure.  In some embodiments, said coordinates include coordinates selected from Appendix 1 and Appendix 2.  Certain embodiments provide a method of producing an enzyme which has increased activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in the catalysis of conversion. 3-methyl-3-buten-2-ol to isoprene comprising: identifying reactive amino acid functional groups and functional group geometry to catalyze said reaction, thereby building an active site; constructing a set of amino acid rotamers from a structural library in which the rotamers incorporate said functional groups and said functional group geometry; the computer identification of an active site placement in a set of candidate protein backbones by a hashing algorithm, wherein the set of amino acid rotamers comprising said active site placement is placed on a candidate protein backbone of so that the active site satisfies the stereochemistry of the protein and maintains a catalytic geometry; Computer selection of an amino acid sequence adapting to the identified backbone and the placed active site, thereby identifying a hypothetical enzyme; the production of the hypothetical enzyme and the confirmation of the activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in catalyzing the conversion of 3-methyl-3-methyl- buten-2-ol in isoprene.  In some embodiments, said enzyme is improved from an LDH / cdLD described herein.  As regards all the above embodiments and the claims, it is also within the scope of the present description all the embodiments which provide an amino acid sequence identity of at least X. % with SEQ ID NO: 1 "instead of" amino acid sequence homology of at least X% with SEQ ID NO: 1 ", X being any of the% used in the present description and claims in the context of sequence homology.  The following example is proposed in this regard, but many other embodiments exist for embodiments in which the term "homology" is replaced by "identity," wherein certain embodiments provide a polypeptide comprising an amino acid sequence having an amino acid sequence identity of at least 90% with SEQ ID NO: 1, said amino acid sequence comprising at least one, preferably one to five, mutations at the following X positions of SEQ ID NO: 1 R1_96X96R97-98X99R100-122X123R124-186X187R188-203X204 R205-211X212R213-272X273X274X275 R276-323X324 R325-327X328R329-R359X360R361-365X366R367-381X382R383-398, wherein: X96 is mutated to a different amino acid selected from L and equivalent amino acids; X99 is mutated to a different amino acid selected from L and equivalent amino acids; X123 is mutated to a different amino acid selected from I and equivalent amino acids; X167 is mutated to a different amino acid selected from M and equivalent amino acids; X204 is mutated to a different amino acid selected from I and equivalent amino acids; X212 is mutated to a different amino acid selected from F, Y, and equivalent amino acids; X273 is mutated to a different amino acid selected from C and equivalent amino acids; X274 is mutated to a different amino acid selected from F and equivalent amino acids; X275 is mutated to a different amino acid selected from I and equivalent amino acids; X324 is mutated to a different amino acid selected from L, E, and equivalent amino acids; X328 is mutated to a different amino acid selected from V and equivalent amino acids; X380 is mutated to a different amino acid selected from Y and equivalent amino acids; X388 is mutated to a different amino acid selected from V, C, G, and equivalent amino acids; X382 is mutated to a different amino acid selected from W and equivalent amino acids; and each R is identical to the corresponding amino acid in SEQ ID NO: 1.  In another embodiment, the identity with SEQ ID NO: 1 is at least 91, at least 92, at least 93, at least 94, at least 95, at least 96, at least 97, at least 98 or at least 99%.  Other objects, features and advantages of the disclosed methods, systems and compositions will become apparent from the following detailed description.  It will be understood, however, that the detailed description and specific examples, while indicating specific embodiments, are given by way of illustration only because various changes and modifications in the spirit and scope of the invention proposed herein will be apparent to the reader. skilled in the art from this detailed description.
[0003] BRIEF DESCRIPTION OF THE DRAWINGS Those skilled in the art will understand that the drawings described below are presented for illustrative purposes only. The drawings are in no way intended to limit the scope of the present teachings. The patent or the application file contains at least one color drawing. Copies of this patent or the publication of the patent application with color drawing (s) will be provided by the United States Patent and Trademark Office upon request and payment by the United States Patent and Trademark Office. tax required. Figure 1: Overview of the cdLD structural architecture, based on the high resolution structure obtained by X-ray crystallography. FIG. lA: symmetrical pentameric arrangement observed in the crystalline structure. FIG. 1 B: cdLD monomer with underlined secondary structure. The alpha 5 helices are in red, the beta strands in yellow and the loops in green. cdLD adopts a folding a / a (6) in barrel. The inner helices of the barrel liner are marked. Figure 2: location of the hypothetical active site at the interface between subunit A and subunit E. Green board: chain A. Light brown: chain B. The side chains covering the hypothetical active site are highlighted. The polar groups in the active site are in pink. Note the distal disulfide bridge (salmon bars) on the left side of the A chain. The view is facing the entrance into the cavity of the active site. [0144] FIG. 3: representation of the secondary structure of cdLD (SEQ ID NO: 87) assigned by the DSSP program and represented with Polyview. The helices (0, 310 and CI) are represented in red cylinders, the strands with the green arrows and the loops in blue threads. The helices were numbered consecutively from the N-terminal region to C-terminal. Figure 4: Butadiene produced by selected periplasmic cdLD mutants obtained from the stabilization scheme. Figure 5: Production of butadiene by some mutants of the second group of site saturation banks. Figure 6: Production of butadiene by mutants formed on the top of A324 L. Figure 7: Production of butadiene by mutants formed on the basis of M274F. Figure 8: production of butadiene by mutants formed on the basis of S366V. [0150] Figure 9: Butadiene production by mutants formed on the basis of V275I. Figure 10: Production of butadiene by mutants formed on the basis of F382W. Figure 11: Butadiene production by some purified periplasmic mutants of cdLD. [0153] FIG. 12: FIG. 12A, production of butadiene from 3-buten-2-ol (10 mM); and FIG. 12B, production of isoprene from 3-methyl-3-buten-2-ol (10 mM) by some purified mutants. 13: relative production of butadiene by combinatorial mutants (test at 1 ml). Figure 14: Relative production of butadiene by combinatorial mutants (test at 1 m1). 15: Butadiene assay with purified cyto-cdLD mutants. Only two clones that showed significant improvement in specific activity compared to wild-type cdLD are presented. 16: pentameric disposition of the cdLD protein monomers in the asymmetric crystal unit. Each polypeptide chain has a unique color. [0158] FIG. 17: FIG. 17A, electronic density associated with the hypothetical active site of cdLD. The blue grid is the 2Fo-Fc map at 1.5 sigma and green, the Fo-Fc map at 3.0 sigma; FIG. 17B: sectional band and surface representation of the hypothetical active site. The modeled zinc atom is a dark gray sphere and all the amino acids in the 6A zinc are presented in stick structures. A black arrow indicates the position and direction of the narrow channel accessible to the solvent. DETAILED DESCRIPTION [0159] All references mentioned are incorporated by reference in their entirety. Unless otherwise indicated, all the technical and scientific terms used herein have the same meaning as that commonly accepted by those skilled in the art for which this description is intended. Unless otherwise indicated, the techniques used or contemplated herein are standard methodologies well known to those skilled in the art. The practice of the present description will, unless otherwise indicated, employ conventional techniques of microbiology, tissue culture, molecular biology, chemistry, biochemistry and recombinant DNA technology which fall within the competencies of the subject. skilled person. The materials, processes and examples are purely illustrative and not limiting. The following data is presented for illustrative purposes and is not intended to limit the scope of the description. Numerous modifications and other embodiments of the description presented herein will be apparent to those skilled in the art to which the present description is intended, taking advantage of the teachings presented in the foregoing descriptions and associated drawings. Therefore, it will be appreciated that the description is not limited to the specific embodiments described and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are used here, they are used in a general and descriptive sense only and not for restrictive purposes. Units, prefixes and symbols may be mentioned in their accepted form in the SI. Unless otherwise indicated, nucleic acids are mentioned from left to right in the 5 'to 3' orientation; amino acid sequences are mentioned from left to right in the amino to carboxy orientation, respectively. Numeric intervals include the numbers defining the interval. The amino acids can be named here either by the three commonly accepted symbolic letters or by one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Similarly, nucleotides may be designated by their commonly accepted single letter codes. The terms defined below are more fully defined with reference to the specification as a whole. In the present specification and claims, conventional one-letter and three-letter codes for amino acid residues are used. For ease of reference, the polypeptides described herein are described using the following nomenclature: amino acid (s) of origin: position (s): substituted amino acid (s) (e.g. , A324L, where A is replaced by L at amino acid position 324). All numbering is effected by reference to the numbering of the wild-type polypeptide of SEQ ID NO: 1 In the present specification and claims, the activity of the claimed polypeptide is measured relative to that of the SEQ ID polypeptide. NO: NO: 1, 4, 5, 7 or 8, unless otherwise indicated. The mutation numbering of each polypeptide described is determined relative to that of the protein of SEQ ID35 NO: 1 (full-length cdLD with two methionines). The homology of the wild-type cdLD polypeptide of SEQ ID NO: 1 is determined without taking into account the presence or absence of a periplasmic label, the presence of one or two initial methionines and the presence or absence of a poly-His tag. In certain embodiments, numbers expressing amounts of ingredients, properties such as molecular weight, reaction conditions and results, etc., used to describe and claim certain embodiments of the present disclosure should be be understood to be modified in some cases by the term "about". In some embodiments, the term "about" is used to indicate that a value includes the standard deviation of the average for the device or process that is used to determine the value. In some embodiments, the numerical parameters indicated in the specification (wherein the claims are incorporated in their entirety) are approximations that may vary depending on the desired properties sought to be achieved by a particular embodiment. In some embodiments, the numeric parameters should be interpreted in light of the number of significant digits reported and by applying the usual rounding principles. Although the numerical intervals and parameters defining the broad scope of some embodiments of the present disclosure are approximations, the numerical values defined in the specific examples are reported as accurately as possible. The numerical values presented in some embodiments of this disclosure may contain some errors resulting from the standard deviation found in the respective test measurements. The enumeration of value ranges in this document is primarily intended for use in an abbreviated process of individual designation of each separate value within that range. Unless otherwise indicated, each individual value is included in the specification as if it had been individually mentioned in this document. As used herein, the term "butadiene" having the molecular formula C4H6 and a molecular weight of 54.09 g / mol (IUPAC name buta-1,3-diene), is used interchangeably with 1,3-butadiene, bi-ethylene, erythrene, divinyl, vinylethylene. Butadiene is a colorless, non-corrosive liquefied gas with a slight aromatic or gasoline-like odor. Butadiene is both explosive and flammable due to its low flash point. The term "conservatively modified variants" applies to both amino acid and nucleic acid sequences. With respect to the particular nucleic acid sequences, conservatively modified variants refer to nucleic acids that encode identical variants or conservatively modified variants of the amino acid sequences. Given the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode a given protein. For example, the GCA, GCC, GCG and GCU codons all encode the amino acid alanine. Therefore, at each position where an alanine is specified by a codon, the codon can be modified to any of the corresponding codons described without modifying the encoded polypeptide. These nucleic acid variations are "silent variations" and represent a conservatively modified species of variation. Each nucleic acid sequence of the present document, which encodes a polypeptide also describes any possible silent variation of the nucleic acid. Those skilled in the art will understand that each codon in a nucleic acid (except AUG, which is usually the only codon for methionine, one exception being Micrococcus rubens, for which GTG is the codon of methionine (Ishizuka, et al., ( 1993) J. Gen. Microbiol 139: 425-32) can be modified to provide a functionally identical molecule, Accordingly, each silent variation of a nucleic acid that encodes a polypeptide of the present disclosure is implicit in each polypeptide sequence described and incorporated herein by reference As regards the amino acid sequences, those skilled in the art will understand that individual substitutions, deletions, or additions to a nucleic acid, peptide, polypeptide, or deprotein which modifies, adds or removes an individual amino acid or a small percentage of amino acids in the coded sequence is a "conservatively modified variant" if the modification results in the substitution of an amino acid with a chemically similar amino acid. Therefore, any number of amino acid residues can be so modified. The conservatively modified variants provide a biological activity equivalent to that of the unmodified polypeptide sequence from which they are derived. Conservative substitution tables providing functionally similar amino acids, also referred to herein as "equivalent amino acids" are well known in the art. The terms "understand", "have" and "include" are open-ended link verbs. Any form or time of one or more of these verbs, such as "includes", "comprising", "a", "having", "includes" and "including" are also open ended. For example, any method that "understands," "a," or "includes" one or more steps is not limited in that it has only this or more steps and may also cover other unlisted steps. Likewise, any composition that "understands", "a" or "includes" one or more features is not limited in that it has only that characteristic or more and may cover other features not listed. All methods described herein may be made in any suitable order unless otherwise indicated herein or if the context clearly indicates otherwise. The use of any and all examples, or illustrative language elements (eg, "such as") provided with respect to certain embodiments of this document is intended merely to further illuminate the present disclosure. and does not constitute a limit of the scope of this description otherwise claimed. No language element of the description shall be considered to indicate as essential for the practice of this description an unclaimed element. As used herein, the term "consisting essentially of" means the inclusion of additional sequences to a polynucleotide or polypeptide in question, the additional sequences not materially affecting the basic function of the polynucleotide or polypeptide sequences. claimed. [0171] "Codon optimization" is the process of modifying a nucleotide sequence in a manner that enhances its expression, G / C content, RNA secondary structure, and translation into eukaryotic cells. , without modifying the amino acid sequence that it encodes. The use of a modified codon is often performed to alter the translational efficiency and / or optimize the coding sequence for expression in a desired host or to optimize the use of the codon in a heterologous sequence for expression. in a particular host. The codon usage in the polynucleotide coding regions of the present disclosure can be analyzed statistically using commercially available software such as "Codon Preference" available from the University of Wisconsin Genetics Computer Group. See Devereaux, et al., (1984) Nucleic Acids Res. 12: 387395) or MacVector 4.1 (Eastman Kodak Co., New Haven, Conn.). Therefore, the present disclosure provides a codon usage frequency characteristic of the coding region of at least one of the polynucleotides of the present disclosure. The number of polynucleotides (3 nucleotides per amino acid) that can be used to determine a codon usage frequency can be any integer of 3 up to the number of polynucleotides of the present description as proposed herein. Optionally, the polynucleotides will be full length sequences. An example of a number of sequences for the statistical analysis can be at least 1, 5, 10, 20, 50 or 100. The term "crystal" refers to a structure (such as a three-dimensional solid aggregate (3D )) in which the planar faces intersect at defined angles and in which there is a regular structure (such as an internal structure) of the constituent chemical species. The term "crystal" refers in particular to a form of solid physical crystal such as an experimentally prepared crystal. Optionally, the cdLD crystal may comprise one or more molecules that bind to the active cdLD site or otherwise impregnate the crystal or are co-crystallized with the cdLD. The term "derivative" includes the terms "from", "obtained" or "likely to be obtained from" and "isolated from". The "equivalent amino acids" can be determined on the basis of either their structural homology with the amino acids for which they are substituted, or the results of comparative tests of biological activity between the various variants that can be generated. By way of non-restrictive example, the list below summarizes the possible substitutions often likely to be carried out without leading to a significant modification of the biological activity of the corresponding variant: 1) Alanine (A), Serine (S), Threonine (T), Valine (V), Glycine (G) and Proline (P); 39 3033 172 2) Aspartic acid (D), glutamic acid (E); 3) Asparagine (N), glutamine (Q); 4) Arginine (R), Lysine (K), Histidine (H); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V) and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W). See also, Creighton, Proteins, W.H. Freeman, and Co. (1984). When these changes / substitutions are made, the hydropathic index of the amino acids can also be taken into account. The importance of the hydropathic index of the amino acid for imparting interactive biological function on a protein is generally understood in the art (Kyte and Doolittle, (1982) J Mol Biol 157 (1): 105-32 ). It is recognized that the relative hydropathic character of the amino acid contributes to the secondary structure of the resulting protein which itself defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA , Antibodies, antigens and the like. It is known in the art that certain amino acids may be replaced by other amino acids having a similar hydropathic index or score and still give a protein exhibiting a similar biological activity, i.e. still obtain a functionally equivalent biological protein. To each amino acid is assigned a hydropathic index based on its hydrophobicity and charge characteristics (Kyte and Doolittle, ibid). These are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine / cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); Histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9) and arginine (-4.5). When making these changes, the substitution of amino acids with hydropathic indexes within +2 is preferred, those within +1 are particularly preferred, and those within +0, Are even more particularly preferred. It will be understood in the art that substitution of similar amino acids can be effected efficiently on the basis of hydrophilicity. U.S. Patent No. 4,554,101 indicates that the highest local average hydrophilicity of a protein, directed by the hydrophilicity of its adjacent amino acids, is correlated with a biological property of the protein. As described in U.S. Patent No. 4,554,101, the following hydrophilicity values were assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 + 0.1); glutamate (+3.0 + 0.1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 + 0.1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2,3); phenylalanine (-2.5); tryptophan (-3.4). In specific embodiments, the substitution is an alanine for the native amino acid on the indicated position (s). The nucleic acid sequence (s) encoding the variant protein or polypeptide (e) are also encompassed. The term "endogenous" with reference to a polynucleotide or protein refers to a polynucleotide or a protein that is naturally present in the host cell. As used herein, the term "expression" refers to the process by which a polypeptide is produced on the basis of the nucleic acid sequence of a gene. The process includes both transcription and translation. An "expression vector" as used herein refers to a DNA construct comprising a DNA sequence that is operably linked to an appropriate control sequence capable of affecting the expression of DNA. in a suitable host. Such control sequences may include a promoter to effect transcription, an optional operator sequence to control transcription, a sequence encoding appropriate ribosome binding sites on mRNA, amplification agents, and sequences that control the end. transcription and translation. Examples of commonly used "expression systems" include recombinant baculovirus, lentivirus, protozory systems (eg, the eukaryotic parasite Leishmania tarentolae), microbial expression systems including yeast-based systems ( eg Pichia Pastoris, Saccharomyces cerevisiae, Yaerobia lipolytica, Hansenula polymorpha, Aspergillus and Trichoderma Fungi) and bacteria-based (e.g., E. Coli, Pseudomonas fluorescens, Lactobacillus, Lactococcus, Bacillus megaterium, Bacillus Subtilis, Brevibacillus, Corynebacterium glutamicum), Chinese hamster ovary cells (CHO), CHOK1SVNSO (Lonza), BHK (baby hamster kidney cells), PerC.6 or Per.C6 (eg, Percivia, Crucell), different HEK cell lines 293, Expi293FTM (Life Technologies), GenScript's YeastHIGH Tm Technology (GenScript), the human neuronal precursor cell line AGE1.HN (Probiogen) and other mammalian cells, plant cells (eg, maize, alfalfa and tobacco), insect cells, eggs, algae and transgenic animals (eg, mice, rats, goats, sheep, pigs, cows). The advantages and disadvantages of these various systems have been reviewed in the literature and are known to those skilled in the art. A "gene" refers to a segment of DNA that is involved in the production of a polypeptide and includes regions preceding and following the coding regions as well as intermediate sequences (introns) between individual coding segments (exons). A "host strain" or "host cell" refers to a suitable host for an expression vector or a DNA construct comprising a polynucleotide encoding a polypeptide as described. Specifically, the host strains may be bacterial cells, mammalian cells, insect cells and other cloning systems or "expression systems". In one embodiment of the disclosure, a "host cell" refers to both cells and protoplasts created from cells of a microbial strain. It will be understood that these terms are intended to denote not only the particular cell in question but the offspring of that cell.
[0004] Since some modifications may occur in successive generations due to mutations or environmental influences, this offspring may in fact not be identical to the parent cell but is still included as part of the term "host cell" such as used here.  The term "heterologous" with reference to a polynucleotide or protein refers to a polynucleotide or a protein / polypeptide that is not present in the natural state.  In some embodiments, the protein is an industrially important protein from a commercial point of view.  It is intended that the term encompasses proteins that are encoded by naturally occurring genes, mutated genes, and / or synthetic genes.  [0187] A polynucleotide or polypeptide having a certain percentage (e.g. , at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99 ° / 0) of sequence identity with another sequence means, when they are aligned, the percentage of bases or amino acid residues that are the same when comparing the two sequences.  When a percentage of sequence identity is used in reference to proteins, it is recognized that residue positions that are not identical often differ by conservative amino acid substitutions when amino acid residues are replaced by other amino acid residues with similar chemical properties (e.g. , charge or hydrophobicity) and therefore, do not modify the functional properties of the molecule.  When the sequences differ in terms of conservative substitutions, the percent sequence identity can be adjusted upward to correct the conservative nature of the substitution and this process gives a "sequence homology" e.g.  at least 90 ° / 0, 91 ° / (:), 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%.  The means for achieving this adjustment are well known in the art.  Usually, this includes determining the score of a conservative substitution as partial rather than a total mismatch, which increases the percentage of sequence identity.  For example, when assigning an identical amino acid, a score of 1 and a non-conservative substitution, a score of zero, a conservative substitution receives a score between zero and 1.  The determination of the conservative substitution score is calculated e.g. according to the algorithm of Meyers and Miller, (1988) Computer Applic.  Biol.  Sci.  4: 11-17, e.g. as implemented in the PC / GENE program (Intelligenetics, Mountain View, Calif. , USA).  This alignment and percentage of homology or identity can be determined using appropriate software known in the art, for example those described in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F.  Mr.  Ausubel et al.  (eds) 1987, Supplement 30, paragraph 7. 7. 18).  These programs may include the GCG Pileup program, FASTA (Pearson et al.  (1988) Proc.  Natl, Acad.  Sci USA 85: 2444-2448), and BLAST (BLAST Manual, Altschul et al. , Nat'l Cent.  Biotechnol.  Inf. , Natl Lib.  Med.  (NCIB NLM NIH), Bethesda, Md. , and Altschul et al. (1997) NAR 25: 3389-3402).  Another alignment program is ALIGN Plus (Scientific and Educational Software, Pa. ), using default settings.  Another sequence software that utilizes the TFASTA data search program is available in the Sequence, Version 6 software. 0 (Genetics Computer Group, University of Wisconsin, Madison, Wis. ).  [0188] The term "introduced" in the context of the insertion of a nucleic acid sequence into a cell, means "transfection," or "transformation," or "transduction," and includes a reference to the incorporation of a nucleic acid sequence into a cell. a nucleic acid sequence in a eukaryotic or prokaryotic cell in which the nucleic acid sequence can be incorporated into the genome of the cell (e.g. , chromosome, plasmid, plastid or mitochondrial DNA), converted to an autonomous replicon or expressed temporarily (e.g. Transfected mRNA).  As used herein, the term "nucleotide sequence" or "nucleic acid sequence" refers to an oligonucleotide or polynucleotide sequence and its variants, homologues, fragments and derivatives.  The nucleotide sequence may be of genomic, synthetic or recombinant origin and may be double stranded or single strand, representing the sense or antisense strand.  As used herein, the term "nucleotide sequence" includes genomic DNA, cDNA, synthetic DNA, and RNA.  The term "nucleic acid" encompasses DNA, cDNA, RNA, heteroduplexes and synthetic molecules capable of encoding a polypeptide.  RNA includes mRNA, RNA, RNAi, siRNA, cRNA and autocatalytic RNA.  The nucleic acids can be single-stranded or double-stranded and there can be chemical modifications.  The terms "nucleic acid" and "polynucleotide" are used interchangeably.  Since the genetic code is degenerate, several codons can be used to code for a particular amino acid and the present compositions and methods include nucleotide sequences that encode a particular amino acid sequence.  A nucleic acid comprises a nucleotide sequence which usually comprises nucleotides comprising an A, G, C, T or U base.  However, the nucleotide sequences may include other bases such as, but not limited to, inosine, methylycytosine, methylinosine, methyladenosine and / or thiouridine, without being limited thereto.  Those skilled in the art will understand that the nucleic acid sequences encompassed by the description are also defined by the ability to hybridize under stringent hybridization conditions with nucleic acid sequences encoding the aforementioned polypeptides. as an example.  A nucleic acid can hybridize to another nucleic acid sequence when a single-stranded form of the nucleic acid can anneal to the other nucleic acid under appropriate conditions of temperature and ionic strength of the solution. .  Hybridization and washing conditions are well known in the art (Sambrook, et al.  (Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory, 4th edition, 2012).  Hybridization under highly stringent conditions means that the temperature and ionic strength conditions are chosen such that they allow hybridization to be maintained between two complementary DNA fragments.  On a purely illustrative basis, the highly stringent conditions of the hybridization step for defining the polynucleotide fragments described above are advantageously as follows.  DNA-DNA or DNA-RNA hybridization is performed in two steps: (1) prehybridization at 42 ° C for three hours in phosphate buffer (20 mM, pH 7.5) containing 5 X SSC (1 X SSC corresponds to a solution of 0.15 M NaCl + 0.015 M sodium citrate), 50% formamide, 7% sodium dodecyl sulphate (SDS), 10 x Denhardt's solution, 5% dextran sulphate and 1% salmon sperm DNA; (2) primary hybridization for 20 hours at a probe-length dependent temperature (ie, 42 ° C for a probe> 100 nucleotides in length) followed by two 20-minute washes at 20 ° C in 2 X SSC + 2% SDS, a 20 minute wash at 20 ° C in 0.1 X SSC + 0.1% SDS.  The last wash is performed in 0.1 X SSC + 0.1% SDS for 30 minutes at 60 ° C for a probe> 100 nucleotides in length.  The highly stringent hybridization conditions described above for a polynucleotide of defined size may be adapted by those skilled in the art for longer or shorter oligonucleotides, according to the procedures described by Sambrook, et al.  (Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory, 3rd edition, 2001).  The stringent conditions can also be obtained with the addition of destabilizing agents such as formamide.  The term "operably linked" and its variants refers to the chemical fusion or bonding or combination of sufficient stability to withstand the conditions encountered in the nucleotide incorporation processes used, 45 between a combination of different compounds, molecules or other entities such as, but not limited to: between a mutant polymerase and a reporter group (e.g. fluorescent dye or nanoparticle); between a nucleotide and a reporter group (e.g. fluorescent dye); or between a promoter and a coding sequence, if it controls the transcription of the sequence.  A "promoter" is a regulatory sequence that is involved in the binding of RNA polymerase to initiate transcription of a gene.  The promoter may be an inducible promoter or a constitutive promoter.  An exemplary promoter used herein is a T7 promoter which is an inducible promoter.  A "periplasmic label" or "periplasmic leader sequence" is an amino acid sequence that, when attached to / present on the N-terminus of a protein / peptide, directs the protein / protein. the peptide to the bacterial periplasm, where the sequence is often removed by a signal peptidase.  Secretion of a protein / peptide in the periplasm may increase the stability of recombinantly expressed proteins / peptides.  An example of a periplasmic label described herein is presented as SEQ ID NO: 3.  The term "recombinant", when used in reference to a cell, a nucleic acid, a protein or a vector, indicates that the cell, nucleic acid, protein or vector has been modified by introduction of a "heterologous nucleic acid" or a protein or alteration of a native or native nucleic acid or protein, or that the cell originates from a cell so modified.  For example, recombinant cells express genes that are not found in the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under-expressed or not expressed at all. .  A "signal sequence" or "signal peptide" refers to an amino acid sequence linked to the N-terminal part of a protein, which facilitates the secretion of the mature form of the protein out of the cell. .  The definition of a signal sequence is a functional sequence.  The mature form of the extracellular protein is devoid of the signal sequence that is cleaved during the secretion process.  A "selective marker" designates a gene capable of expression in a host that allows the selection of these hosts containing a nucleic acid or an introduced vector.  Examples of selectable markers include, but are not limited to, antimicrobials (e.g. , hygromycin, bleomycin or chloramphenicol) and / or genes that confer a metabolic benefit such as a nutritional benefit to the host cell.  A structure that "substantially conforms" to a given group of atomic coordinates is one in which at least about 50% of the structure has an RMSD of less than about 1.5 ANG for the backbone atoms in the structures. secondary structure elements in each domain, and more preferably, less than about 1.3 ANG for the backbone atoms in the secondary structure elements in each domain, and more preferably, less than about 1.0 ANG, less than about 0.7 ANG, less than about 0.5 ANG, and most preferably, less than about 0.3 ANG for the backbone atoms in the secondary structure elements in each domain.  In a more preferred embodiment, a structure which substantially conforms to a given group of atomic coordinates is a structure in which at least about 75% of the structure has the indicated RMSD value and more preferably at least about 90%. of this structure has the indicated RMSD value and most preferably, about 100% of this structure has the indicated RMSD value.  In an even more preferred embodiment, the above definition of "substantially conforming" may be extended to include atoms of the amino acid side chains.  As used herein, the phrase "common amino acid side chains" refers to amino acid side chains that are common to both the structure that conforms to a given group of atomic coordinates and to the structure. which is actually represented by these atomic coordinates.  The phrase "under transcriptional control" is an expression well understood in the art that indicates that transcription of a polynucleotide sequence, typically a DNA sequence, depends on whether it is operably linked to an element. which contributes to the initiation of transcription or promotes it.  The phrase "under translational control" is a well-understood expression in the art that indicates a regulatory process that occurs after mRNA has been formed.  As used herein, the term "transformed cell" includes cells that have been transformed or transduced by the use of recombinant DNA techniques.  The transformation is usually done by inserting one or more nucleotide sequences into a cell.  The inserted nucleotide sequence may be a "heterologous nucleotide sequence", i.e. a sequence that is not natural for the cell to be transformed, such as a fusion protein.  As used herein, the terms "transformed", "stably transformed" and "transgenic" used with reference to a cell means that the cell has a non-native nucleic acid sequence (e.g. , heterologous) integrated into its genome or as an episomal plasmid that is conserved over multiple generations.  [0206] "Variants" refer to both polypeptides and nucleic acids.  The term "variant" may be used interchangeably with the term "mutant".  Variants include insertions, substitutions, transversions, truncations and / or inversions at one or more sites in the amino acid sequence or nucleotide sequence, respectively, of a parent sequence.  The nucleic acid variants may include sequences that are complementary to sequences that are capable of hybridizing to the nucleotide sequences presented herein.  For example, a variant sequence is complementary to sequences capable of hybridizing under stringent conditions (e.g. , 50 ° C and 0.2. X SSC (1 X SSC = 0.15 M NaCl, 0.015 M sodium citrate, pH 7.0)) to the nucleotide sequences presented herein.  More particularly, the term variant encompasses sequences that are complementary to sequences that are capable of hybridizing under highly stringent conditions (e.g. , 65 ° C and 0.1 X SSC) to the nucleotide sequences presented here.  The term "vector" as used herein is intended to refer to a nucleic acid molecule capable of transporting another nucleic acid to which it has been bound.  One type of vector is a "plasmid" that refers to a circular double-stranded DNA loop in which additional DNA segments may be linked.  Another type of vector is a viral vector in which additional DNA segments may be linked in the viral genome.  Some vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. , bacterial vectors having an origin of bacterial replication and episomal vectors of mammals).  Other vectors (e.g. , non-episomal mammalian vectors) can be integrated into the genome of a host cell by introduction into the host cell and are thus replicated with the host genome.  In addition, some vectors are able to direct the expression of the genes to which they are functionally linked.  These vectors are referred to herein as "recombinant expression vectors" (or simply, "expression vectors").  In general, expression vectors useful in recombinant DNA techniques are often in the form of plasmids.  In the present specification, the terms "plasmid" and "vector" can be used interchangeably because the plasmid is the most frequently used vector form.  However, the claimed embodiments are intended to include these other forms of expression vectors such as viral vectors (e.g. replication defective retroviruses, adenoviruses and adeno-associated viruses) that have equivalent functions.  The vectors also include cloning vectors, shuttle vectors, plasmids, phage particles, cassettes, and the like.  [0208] We will now refer in detail to various described embodiments.  The discovery that the cdLD is capable of catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene is described here.  The positive results obtained with the cdLD for catalyzing this reaction with the relatively low catalytic competence exhibited by this wild-type enzyme (WT) have resulted in several attempts to improve the activity of the cdLD.  A crystalline structure or a homology model is a significant aid for the optimization of the enzyme.  However, a deltaBLAST search in the Protein Data Bank (PDB) protein sequence database revealed that the cdLD has no detectable homology with any sequence for which a structural model is available.  Accordingly, the present disclosure also discloses the crystalline structure of apo cdLD, elucidated here by X-ray crystallography.  Purified apo cdLD crystals were obtained, the three-dimensional structure of this enzyme was elucidated for the first time and the results were independently confirmed.  An apo structure of cdLD was then refined successfully to 2.54A with an R value of R = 21.6 () / 0 and R = 26.9%.  The details of this procedure can be found in the Examples section of this description.  [0210] This description has elucidated several areas in the cdLD.  The cdLD crystallized in a P21 space group.  The cdLD adopts a pentameric arrangement with 5-axis axial symmetry in the asymmetric unit (A-E chain).  Each monomer adopts a barrel folding 0/0 (6), a relatively unusual folding that can be seen in Figure 1.  An apparent and notable feature in the crystal structure is that a disulfide bridge is formed between Cys74 and Cys127 of each subunit (crystal structure count).  A search for structural homology using the DALI program gives various structural counterparts.  The structural alignment between monomeric cdLD and some of the DALI candidates reveals that enzymes that are structurally homologous to cdLD all have their active sites at the "top" of the barrel with the catalytic residues supported by the internal helices that coat the interior of the barrel. barrel (propellers 4, 7, 9, 11, 13, 14) and the loops connecting these propellers to the external propellers of the barrel.  Consistent with other enzymes that adopt similar folding, cdLD has a marked slot in this same region while the rest of the subunit is fully exposed to the solvent in a tightly compact manner.  Therefore, we hypothesized that the likely position of the active site of the cdLD responsible for the observed catalytic activity is located in this region.  Unlike most cdLD structural counterparts, this hypothetical active site is formed at the interface between subunits, for example, A and B in FIG.  The 62-77 (crystal structure numbering) loop of subunit B protrudes and closes the pocket formed by the top of the sub-unit A barrel, see FIGURE 2.  The elucidation of cdLD crystalline structure data provides a better understanding of cdLD enzymatic activity and the intelligent design of many enhancements thereof as well as the development of various compounds that act as substrates or cdLDs. cdLD inhibitors or polypeptides described herein.  In one embodiment, the description has identified the catalytic residues of the cdLD.  Accordingly, the disclosure provides compounds that bind to the catalytic site of the cdLD and are identified using the structural data described herein and / or any suitable method described herein.  The candidate compounds identified using the structural data described herein may be any suitable compound, including naturally occurring compounds, de novo designed compounds, library generated compounds, 3- butane-2-01 (3B20) and analogs thereof and include organic compounds, novel chemical entities, among others.  One skilled in the art can use one of the many methods for screening entities (whether chemical or protein) for their ability to associate with the cdLD or polypeptides described herein.  Specialized software can also help with the entity selection process.  These include: GRID (Goodford, A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules, J.  Med.  Chem. , 28, pp.  849-857 (1985)).  GRID is available from Oxford University, Oxford, UK; MCSS (Miranker et al. , "Functionality.  Maps of Binding Sites: A Multiple Copy Simultaneous Search Method.  Proteins: Structure, Function and Genetics, 11, pp.  29-34 (1991)).  MCSS is available from Molecular Simulations, San Diego, Calif.  ; AUTODOCK (Goodsell et al. , "Automated Docking of Substrates to Proteins by Simulated Annealing," Proteins: Structure, Function, and Genetics, 8, pp.  195-202 (1990)).  AUTODOCK is available from Scripps Research Institute, La Jolla, Calif.  ; & DOCK (Kuntz et al. , "A Geometric Approach to Macromolecule-Ligand Interactions," J.  Mol.  Biol. , 161, pp.  269-288 (1982)).  DOCK is available from the University of California, San Francisco, Calif.  In another embodiment, the disclosure relates to a method of synthesizing or obtaining a candidate compound designed or screened for binding to cdLD or one of the polypeptides described herein and then determining the ability of the candidate compound to interact with any of these proteins.  In another embodiment, the description relates to the subgroups of the atomic coordinates listed in Appendix I and the subgroups which substantially conform to them.  Preferred subgroups 513033172 define one or more cdLD regions selected from those listed in Table 3 and FIGURE 3.  The present invention also provides subgroups of the atomic coordinates listed in Appendix I.  The coordinates mentioned here include Cartesian coordinates derived from the mathematical equations associated with the patterns obtained on the diffraction of a monochromatic X-ray beam by the atoms of a protein or protein complex in crystalline form.  The diffraction data are used to calculate an electronic density map of the crystal repeating units.  The electronic density maps are then used to establish the positions of the individual atoms of the molecule or molecular complex.  In one embodiment, a machine-readable data storage medium is provided comprising a data storage material encoded with machine-readable data which, when used by a programmed machine with instructions for using said data, displays a three-dimensional graphical representation comprising a cdLD or a polypeptide described herein.  It will be understood that a group of structural coordinates for a polypeptide is a group of relative points that define a three-dimensional shape.  It is therefore possible for a group of entirely different coordinates to define a similar or identical shape.  In addition, slight variations in the individual coordinates will have little effect on the overall shape.  These groups of coordinates are also embodiments within the scope of the present description.  [0218] Coordinate variations can be generated by mathematical manipulations of structural coordinates.  For example, the structural coordinates defined in Annex I could be manipulated by crystallographic permutations of structural coordinates, splitting of structural coordinates, addition or subtraction of integers to structural coordinate groups, inversion of structural coordinates or any other structural coordinates. combination of these.  Alternatively, a modification of the crystal structure due to mutations, additions, substitutions, and / or deletions of amino acids or other changes in any of the components that make up crystal 52 could also constitute variations in structural coordinates.  These variants are also embodiments within the scope of the present description.  In one embodiment, the structural coordinates defined herein may also be used to help obtain structural information on another crystallized molecule or molecular complex.  This can be achieved by any of the many well known techniques including molecular replacement.  For example, a method is also provided for using molecular replacement to obtain structural information on a protein whose structure is unknown, including the steps of: generating an X-ray diffraction pattern of a crystal of the protein whose structure is unknown; generating a three-dimensional electronic density map of the protein whose structure is unknown to the X-ray diffraction pattern by using at least a portion of the structural coordinates defined herein as a molecular replacement pattern.  By using the molecular replacement, all or part of the cdLD structural coordinates provided by the present description (and defined in the appended figures) can be used to determine the structure of another crystallized molecule or of another complex. more quickly and efficiently than by trying to determine the structure initially.  One particular use includes use with other structurally similar proteins.  Molecular replacement ensures accurate estimation of the phases of an unknown structure.  Phases are a factor in the equations used to solve crystal structures that can not be determined directly.  Obtaining accurate values for the phases by methods other than molecular replacement is a time-consuming process involving iterative cycles of approximations and refinement and greatly hinders the solution of crystalline structures.  However, when the crystal structure of a protein containing at least one homologous portion has been resolved, the phases of the known structure provide a satisfactory estimate of the phases for the unknown structure.  Therefore, this method involves generating a preliminary model of a molecule or molecular complex whose structural coordinates are unknown, by orienting and positioning the relevant part of the cdLD according to the accompanying figures in the unit cell of the crystal of the molecule or unknown molecular complex to better take into account the observed X-ray diffraction pattern of the crystal of the molecule or molecular complex whose structure is unknown.  The phases can then be calculated from this model and combined with the observed X-ray diffraction pattern amplitudes to generate an electronic density map of the structure whose coordinates are unknown.  This may itself be subject to the development of a well-known model and structural refinement techniques to give a precise final structure of the crystallized molecule or unknown molecular complex (Lattman, "Use of the Rotation and Translation Functions ", in Meth.  Enzymol. , 115, pp.  55-77 (1985); Rossmann, ed. , The Molecular Replacement Method, Int.  Sci.  Rev.  Ser. , No. 13, Gordon & Breach, New York (1972)).  The structural coordinates of the cdLD as provided by the present disclosure are useful for resolving the structure of polypeptides that have amino acid substitutions, additions, and / or deletions relative to the naturally occurring cdLD.  These polypeptides may optionally be crystallized in a co-complex with a ligand, such as an inhibitor or substrate analogue.  The crystal structures of a series of these complexes can then be resolved by molecular replacement and compared with those of the cdLD.  Potential sites of modification in the various binding sites of the enzyme can then be identified.  This information provides an additional tool for determining the most effective binding interactions, such as, for example, increased hydrophobic interactions between cdLD and a ligand.  It should be noted that the ligand may be the natural ligand of the protein or may be a substrate or a potential inhibitor of the protein.  In the present specification and claims, the newly described polypeptides which exhibit increased activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or in the catalysis of 3-methyl 3-buten-2-ol in isoprene are described and claimed.  In some embodiments, said enhancement can be observed in vivo.  In other embodiments, said increase can be observed in the purified polypeptide, in which case the enhancement refers to an increase in specific activity.  In some embodiments, the improved polypeptides are expected to exhibit said increased activity, whether or not they have a periplasmic tag and / or a C-terminal poly-His tag.  In other embodiments, it is also contemplated that the improved polypeptides have increased activity relative to cdLD of SEQ ID NO: 1, 4, 5, 7 or 8.  It will be understood that conservatively modified variants of the polypeptides specified herein are also within the scope of this disclosure.  The following is presented the relationship between mutations that may be present in the polypeptides described herein and desirable modifications of the properties (relative to those of the wild-type polypeptide of SEQ ID NO: 1, 4, 5, 7 or 8).  [0225] In vivo improved activity in the catalysis of dehydration of 3-buten-2-01 to 1,3-butadiene [0226] Certain embodiments provide polypeptides having improved activity in the catalysis of dehydration of 3-butenediol. 2-ol to 1,3-butadiene, based on the polypeptide of SEQ ID NO: 1, 4, 5, 7 or 8.  The improved activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene can be measured by any method known to those skilled in the art.  In one embodiment, the improved activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene of a polypeptide described herein refers to increased activity in the catalysis of 3-butenal dehydration. -2-ol to 1,3-butadiene of a bacterial cell culture expressing said polypeptide, relative to a bacterial cell extract expressing a wild-type polypeptide of SEQ ID NO: 1, 4, 5, 7 or 8.  In certain embodiments, the activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene is at least 80% of that of a polypeptide consisting of SEQ ID NO : 1, 4, 5, 7 or 8, increased by a factor of about 1.5 or greater over that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably, a factor 2 about or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8; preferably about 2.5 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 3 fold or greater with respect to that of a polypeptide consisting of SEQ ID NO: 1, 4, 7 or 8, preferably about 3.5 fold higher than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably by a factor of about 45 or greater relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably a factor of 4 , About or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, or preferably about 5 fold or greater than that of a polypeptide consisting of of SEQ ID NO: 1, 4, 5, 7 or 8, and the activity being observed in at least one activity assay.  In certain embodiments, the increase in catalysis of the dehydration of 3-buten-2-ol to 1,3-butadiene is observed in at least one type of non-bacterial cell expressing a polypeptide of SEQ ID NO : 1.4, 5, 7 or 8.  In some embodiments, the increase in catalysis of the dehydration of 3-buten-2-ol to 1,3-butadiene is observed in at least one type of bacteria.  In some embodiments, the increase in catalysis of dehydration of 3-buten-2-ol to 1,3-butadiene is observed in more than one type of bacteria.  In some embodiments, the bacteria are a strain of E.  Coll.  In some embodiments, the bacteria are Origami2 (DE3).  In some embodiments, the bacteria are BL21 (DE3).  [0229] Enhanced specific activity in the catalysis of dehydration of 3-buten-2-ol to 1,3-butadiene [0230] Some embodiments provide polypeptides with enhanced specific activity in the catalysis of dehydration of 3- buten-2-ol to 1,3-butadiene, based on the polypeptide of SEQ ID NO: 1, 4, 5, 7 or 8.  The specific activity improved in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene can be measured by any method known to those skilled in the art.  In one embodiment, the improved specific activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene of a polypeptide described herein refers to an increased specific activity in the catalysis of dehydration of 3 -buten-2-ol to 1,3-butadiene of the purified polypeptide, relative to that of the purified polypeptide of SEQ ID NO: 1, 4, 5, 7 or 8.  In some embodiments, the specific activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene is at least 80% of that of a polypeptide consisting of SEQ ID. NO: 1, 4, 5, 7 or 8, increased by a factor of about 1.5 or greater relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably by a factor of about 2 or greater over that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8; preferably about 2.5 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8: preferably about 3 fold or greater over that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 3.5 fold higher than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably by a factor of about 4 or more with respect to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably a factor of About 4.5 or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, or preferably about 5 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, and the activity being observed in at least one specific activity assay.  In certain embodiments, the increase in catalysis of the dehydration of 3-buten-2-ol to 1,3-butadiene is observed in polypeptides purified from at least one type of non-bacterial cell. expressing a polypeptide of SEQ ID NO: 1, 4, 5, 7, or 8.  In some embodiments, the increase in catalysis of the dehydration of 3-buten-2-ol to 1,3-butadiene is observed in polypeptides purified from at least one type of bacteria.  In some embodiments, the increase in catalysis of the dehydration of 3-buten-2-ol to 1,3-butadiene is observed in polypeptides purified from more than one type of bacteria.  In some embodiments, the bacteria are a strain of E.  coli.  In some embodiments, the bacteria are Origami2 (DE3).  In some embodiments, the bacteria are BL21 (DE3).  It will be appreciated that additional embodiments include polypeptides where it may be advantageous to introduce additional point mutations (e.g. , deletions, insertions, inversions, substitutions) in any of the polypeptides described herein.  Any of the polypeptides described herein may contain or be devoid of an N-terminal periplasmic label.  In some embodiments, the periplasmic tag (SEQ ID NO: 3) is the underlined sequence in the protein of SEQ ID NO: 1.  In one embodiment, the polypeptide may contain a C-terminal tag.  In some embodiments, the C-terminus tag is a poly-histidine tag consisting of six histidines 57 (SEQ ID NO: 10), with or without additional amino acids, such as in SEQ ID NO: 4 and 5.  In some embodiments, the polypeptide contains both a periplasmic tag and a C-terminal tag.  In some embodiments, the polypeptide contains only a periplasmic tag.  In some embodiments, the polypeptide contains a C-terminal tag.  In any of these embodiments, the C-terminal tag may be a poly-histidine tag.  In some embodiments, the C-terminal tag is that of SEQ ID NO: 6.  In one embodiment, the amino acid sequence of the polypeptide is that of any of the polypeptides listed in the sequence listing in the Examples section.  In related embodiments, the polypeptide lacks the poly-His tag.  In related embodiments, the polypeptide is devoid of the periplasmic tag.  In related embodiments, the polypeptide lacks the periplasmic tag and the poly-His tag which can be that of SEQ ID NO: 6 or just HHHHHH (His6) (SEQ ID NO: 10).  Derivatives of the polypeptides described herein are also provided.  In one embodiment, the derived polypeptides are polypeptides that have been modified, for example by conjugation or complex formation with other chemical moieties, by posttranslational modification (e.g.  phosphorylation, acetylation and others), a change in glycosylation (e.g.  addition, removal or modification of glycosylation), and / or inclusion / substitution of additional amino acid sequences as understood in the art.  Additional amino acid sequences may include fusion partner amino acid sequences that create a fusion protein.  By way of example, the fusion partner amino acid sequences may assist in the detection and / or purification of the isolated fusion protein.  Non-limiting examples include metal binding melt partners (e.g.  poly-histidine), maltose binding protein (MBP), protein A, glutathione S-transferase (GST), fluorescent protein sequences (e.g.  GFP), epitope tags such as myc, FLAC and haemagglutinin tags.  Other derivatives contemplated by the embodiments include, but are not limited to, side chain modification, incorporation of unnatural amino acids and / or their derivatives during peptide or protein synthesis. and the use of crosslinking agents and other methods that impose conformational constraints on the disclosed polypeptides and fragments.  [0240] Embodiments also include nucleic acid molecules encoding relatives of the disclosed polypeptides.  The term "parent" of the nucleic acid sequences encoding the disclosed polypeptide includes the sequences that encode the polypeptides described herein but which differ in a conservative manner due to degeneracy of the genetic code.  Allelic polypeptides that subsequently grow in culture can be identified using well-known molecular biology techniques, such as polymerase chain reaction (PCR) and hybridization techniques as set forth below.  The parent nucleic acid sequences also include synthetically obtained nucleic acid sequences that have been generated, for example, using site-directed mutagenesis but still encode the described polypeptides.  Those skilled in the art will further understand that changes may be introduced by mutation of the nucleic acid sequences thus resulting in changes in the amino acid sequence of the encoded polypeptides without altering the biological activity of the proteins.  Therefore, parent nucleic acid molecules can be created by introducing one or more nucleotide substitutions, nucleotide additions and / or nucleotide deletions into the corresponding nucleic acid sequence described herein, so that one or more substitutions of amino acids, amino acid additions or deletions of amino acids are introduced into the encoded protein.  Mutations can be introduced by standard techniques such as site-directed mutagenesis and PCR-mediated mutagenesis.  These parent nucleic acid sequences are also encompassed in the present embodiments.  Alternatively, variants of nucleic acid sequences may be produced by introducing mutations randomly into all or part of the coding sequence, e.g.  by saturation mutagenesis and the mutants obtained can be screened for the ability to confer increased activity or increased specific activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene to identify mutants which retain the increased activity of the polypeptides described herein.  After mutagenesis, the encoded protein can be expressed recombinantly and the activity of the protein can be determined using standard assay techniques, including those described herein.  Nucleic Acids [0243] With the polypeptides described herein and their amino acid sequence as described herein, those skilled in the art can determine suitable polynucleotides that encode these polypeptides.  Those skilled in the art will readily understand that in view of the degeneracy of the genetic code, there are multiple nucleotide sequences encoding the polypeptides described herein.  The sequence of the polynucleotide gene can be deduced from a polypeptide sequence by the use of the genetic code.  Software such as "BackTranslate" (GCGTM Package, Acclerys, Inc.  San Diego, Calif. ) can be used to convert a peptide sequence into the corresponding nucleotide sequence coding for the peptide.  In addition, synthetic variants of the polynucleotide sequences encoding the polypeptides described herein may be designed to be expressed in any cell type, prokaryotic or eukaryotic.  [0245] Accordingly, certain embodiments relate to polynucleotides comprising or consisting essentially of a nucleic acid sequence encoding a polypeptide as described above and in other parts of this document.  In some embodiments, the nucleic acid sequence is a DNA sequence (e.g. a cDNA sequence).  In other embodiments, the nucleic acid sequence is an RNA sequence.  In some embodiments, the nucleic acid is a cDNA encoding any of the polypeptides described herein.  The nucleotide sequences encoding the polypeptide may be prepared by any suitable technology well known to those skilled in the art, including, but not limited to, recombinant DNA technology and chemical synthesis.  Synthetic polynucleotides can be prepared by commercially available automatic polynucleotide synthesizers.  [0246] One aspect relates to isolated or recombinant nucleic acid molecules comprising nucleic acid sequences encoding the polypeptides described herein or biologically active portions thereof, as well as nucleic acid molecules sufficient to be used as hybridization probes to identify nucleic acid molecules encoding proteins having regions of sequence homology with the polypeptides described herein.  Nucleic acid molecules that are fragments of these nucleic acid sequences encoding polypeptides are also encompassed in the embodiments.  A "fragment" refers to a portion of the nucleic acid sequence encoding a portion of a polypeptide.  In some embodiments, a nucleic acid sequence fragment may encode a biologically active portion of a polypeptide or it may be a fragment that can be used as a hybridization probe or a PCR primer using well-established methods. known to those skilled in the art.  In some embodiments, the nucleic acid has been subjected to codon optimization for the expression of any of the polypeptides described herein.  In other embodiments, the nucleic acid is a probe which may be a single-stranded or double-stranded oligonucleotide or polynucleotide, appropriately labeled to detect complementary sequences of polynucleotides encoding the polypeptides described herein. such as in fleas, or a Northern blot or Southern blot technique.  Methods for detecting labeled nucleic acids hybridized to an immobilized nucleic acid are well known to those skilled in the art.  These methods include autoradiography, chemiluminescence detection, fluorescence and colorimetry.  In some embodiments, the polynucleotide comprises a sequence encoding one of the polypeptides described herein, operably linked to a promoter sequence.  Constitutive or inducible promoters known in the art are contemplated herein.  The promoters may be naturally occurring promoters or hybrid promoters that combine elements of multiple promoters.  Non-limiting examples of promoters include the SV40, cytomegalovirus (CMV) and HIV-1 LTR promoters.  In some embodiments, the polynucleotide comprises a sequence encoding any of the polypeptides described herein, operably linked to a coding sequence for another protein that may be a fusion protein or other protein separated by a link segment.  In some embodiments, the linker has a protease cleavage site such as factor Xa or thrombin, which allows the protease in question to partially digest the fusion polypeptide described herein and thereby release it from the the recombinant polypeptide.  The released polypeptide can then be isolated from the fusion partner, for example, by subsequent chromatographic separation.  In some embodiments, the polynucleotide comprises a sequence encoding any of the polypeptides described herein, operably linked to both a promoter and a fusion protein.  [0251] Certain other embodiments provide genetic constructs in the form of or comprising genetic components of a plasmid, bacteriophage, cosmid, yeast or artificial chromosome of a bacterium, as will be understood in the art.  Genetic constructs may be suitable for the conservation and propagation of isolated nucleic acid in bacteria or other host cells, for manipulation by recombinant DNA technology and / or expression (expression vectors ) of the nucleic acid or encoded polypeptide as described herein.  Some other embodiments relate to recombinant expression vectors comprising a DNA sequence encoding one or more of the polypeptides described herein.  In some embodiments, the expression vector comprises one or more of said linked DNA sequences functioning with a promoter.  Suitably, the expression vector comprises the nucleic acid encoding one of the polypeptides described herein, operably linked to one or more additional sequences.  In some embodiments, the expression vector may be a self-replicating extrachromosomal vector such as a plasmid or vector that integrates into a host genome.  Non-limiting examples of viral expression vectors include adenoviral vectors, adeno-associated virus vectors, herpesvirus vectors, retroviral vectors, lentiviral vectors, and the like.  For example, the adenoviral vectors may be first, second, third and / or fourth generation adenoviral vectors or "gutless" adenoviral vectors.  Adenoviral vectors can be generated at very high levels of infectious particles, infect a wide variety of cells, efficiently transfer genes to cells that do not divide, and are rarely integrated into the host genome, thereby avoiding the risk of cell transformation by insertion mutagenesis.  The vector may further comprise sequences flanking the RNA-yielding polynucleotide that includes sequences homologous to eukaryotic or viral genomic genomic sequences.  This allows the introduction of the polynucleotides described herein into the genome of a host cell.  An integrative cloning vector may be integrated randomly or on a predetermined target locus in the chromosome (s) of the host cell in which it is to be integrated.  Specific embodiments of expression vectors can be found elsewhere in this specification (see below).  [0255] Certain other embodiments relate to host cells comprising a DNA molecule encoding a polypeptide as described herein.  In some embodiments, these host cells may be described as expression systems.  Host cells suitable for expression may be prokaryotic or eukaryotic cells.  Non-restrictively, the appropriate host cells may be mammalian cells (e.g.  HeLa cells, HEK293T, Jurkat), yeast cells (e.g.  Saccharomyces cerevisiae), insect cells (e.g.  Sf9, Trichoplusia ni) used with or without baculovirus expression system or bacterial cells such as E. coli.  neck / (Origami2 (DE3), BL21 (DE3)) or a host virus Vaccinia.  The introduction of genetic constructs into host cells (whether prokaryotic or eukaryotic) is well known in the art, as described, for example, by Current Protocols in Molecular Biology Eds.  Ausubel et al. , (John Wiley & Sons, Inc.  current update July 02, 2014).  Another embodiment relates to a transformed or transduced organism such as an organism chosen from plant and insect cells, bacteria, yeasts, baculoviruses, protozoa, nematodes, algae and transgenic mammals (mice, rats, pigs, etc. ).  The transformed organism comprises a DNA molecule of the embodiments, an expression cassette comprising the DNA molecule or a vector comprising the expression cassette that can be stably incorporated into the genome of the transformed organism .  Methods for Preparing Polypeptides [0257] The polypeptides described herein (including fragments and derivatives) can be prepared by any suitable procedure known to those skilled in the art.  In some embodiments, the protein is a recombinant protein.  By way of example only, a recombinant polypeptide may be produced by a method comprising the steps of: (i) preparing an expression construct which comprises a nucleic acid expressing one or more of the polypeptides described herein, linked functionally to one or more regulatory nucleotide sequences; (ii) transfection or transformation of a suitable host cell with the expression construct; (iii) expressing a recombinant polypeptide / protein (e) in said host cell; and (iv) isolating the recombinant polypeptide / protein from said host cell or using the host cell obtained as such or as a cell extract.  Several methods of introducing mutations into genes, cDNAs and other polynucleotides are known in the art, including the use of commercially available deposited library generation methods.  The DNA sequence encoding a wild-type polypeptide of SEQ ID NO: 1 (with or without one of the first two Met) may be isolated from any cell or microorganism producing the polypeptide in question, using various methods well known in the art.  In one embodiment, the cDNA encoding the wild-type polypeptide of SEQ ID NO: 1 (with or without one of the first two Met) is obtained from Castellaniella defragrans cells, cDNA libraries or other.  In one embodiment, the mutations are introduced into a wild-type polypeptide of SEQ ID NO: 1 (or SEQ ID NO: 1 without the periplasmic tag or SEQ ID NO: 4 or 5) using mutagenesis. directed.  Once a DNA sequence encoding the wild type polypeptide has been isolated and desirable mutation sites have been identified, the mutations can be introduced using synthetic oligonucleotides.  These oligonucleotides contain nucleotide sequences flanking the desired mutation sites; the mutant nucleotides are inserted during the synthesis of the oligonucleotide.  In a specific method, a single-stranded DNA clipping, covering the coding sequence for the polypeptide, is created in a vector carrying the gene encoding the wild-type polypeptide of SEQ ID NO: 1 (or SEQ ID NO: 1 without the periplasmic label or SEQ ID NO: 4 or 5).  Then, the synthetic nucleotide carrying the desired mutation is annealed to a homologous portion of the single-stranded DNA.  The remaining cleavage is then filled with DNA polymerase I (Klenow fragment) and the construct is ligated using T4 ligase.  Another embodiment for introducing mutations into the DNA sequences coding for the wild-type polypeptide SEQ ID NO: 1 (or SEQ ID NO: 1 without the periplasmic tag or SEQ ID NO: 4 or 5). ) comprises the 3-step generation of a PCR fragment containing the desired mutation introduced using a chemically synthesized DNA strand as one of the primers in the PCR reactions.  From the PCR-generated fragment, a DNA fragment carrying the mutation can be isolated by cleavage with restriction endonucleases and reinserted into an expression plasmid.  [0263] Expression of the polypeptides [0264] In one embodiment, the polypeptides are expressed according to the methods described in the Examples section of the present description.  According to certain other embodiments, a DNA sequence encoding the polypeptide produced by methods described above or produced by other methods known in the art, can be expressed, in enzymatic form, using a DNA vector. expression which usually comprises control sequences encoding a promoter, an operator, a ribosomal binding site, a translation initiation signal and optionally, a repressor gene or various activator genes.  For each combination of a promoter and a host cell, culture conditions are available which result in the expression of the DNA sequence encoding the desired polypeptide.  After reaching the desired density or cell size of the polypeptide, the culture is stopped and the polypeptide is recovered using known procedures.  Alternatively, the host cell is used directly (e.g. , pellet, suspension), that is to say without isolation of the recombinant protein.  The recombinant expression vector carrying the DNA sequence encoding a polypeptide as described herein can be any vector that can be appropriately subjected to recombinant DNA procedures and the choice of a vector will often depend on of the host cell into which it is introduced.  Therefore, the vector may be an autonomously replicating vector, i.e. a vector that exists as an extrachromosomal entity whose replication is independent of chromosomal replication, e.g. , a plasmid, a bacteriophage or an extrachromosomal element, a minichromosome or an artificial chromosome.  Alternatively, the vector may be a vector which, when introduced into a host cell, is integrated into the genome of the host cell and replicated together with the chromosome (s) in which it has been integrated.  In the vector, the DNA sequence is usually operably linked to a suitable promoter sequence.  The promoter may also be a DNA sequence that exhibits transcriptional activity in the selected host cell and can be derived from genes encoding homologous or heterologous proteins at the host cell.  Examples of suitable promoters for directing the transcription of the DNA sequence encoding a polypeptide as described herein, in particular, in a bacterial host, are promoters of the E. lac operon.  neck, promoters of the dagA gene of Streptomyces coelicolor, promoters of Castellaniella defragrans, and others.  For transcription in a fungal host, examples of useful promoters are those derived from the gene encoding A. TAKA amylase.  oryzae amylase, aspartic proteinase of Rhizomucor miehei, neutral LDH of A.  freeze, stable acid LDH from A.  freeze, the glucoamylase of A.  freeze, the lipase of Rhizomucor miehei, the alkaline protease of A.  oryzae, the triose phosphate isomerase of A.  oryzae or A. acetamidase.  nidulans.  Promoters can be chosen on the basis of the desired result.  The nucleic acids may be combined with constitutive, tissue-preferred, inducible promoters, or other expression promoters in the host cell or organism.  The list of promoters above is not intended to be restrictive.  Any suitable promoter can be used in the embodiments.  In some embodiments, the expression vector described may also include an appropriate transcription terminator and in eukaryotes, polyadenylation sequences operably linked to the DNA sequence encoding the polypeptide as described herein.  The termination and polyadenylation sequences may or may not be appropriately derived from the same sources as the promoter.  In some embodiments, the vector may further comprise a DNA sequence allowing the vector to replicate in the host cell 66 in question.  Examples of these sequences are the origins of replication of plasmids pUC19, pACYC177, pUB110, pE194, pAMB1 and pIJ702.  The above list of origins of replication is not meant to be restrictive.  Any suitable origin of replication can be used in the embodiments.  In some embodiments, the vector may also include a selectable marker.  The selectable marker genes are used for the selection of transformed cells or tissues, e.g. , a gene whose product completes a defect of the host cell such as dal genes of B.  subtilis or B.  licheniformis, or a gene that confers antibiotic resistance such as resistance to ampicillin, kanamycin, chloramphenicol, or tetracycline.  In addition, the vector may include Aspergillus selection markers such as amdS, argB, niaD and sC, a hygromycin resistance-inducing marker, or selection may be effected by cotransformation.  The above list of selectable marker genes is not intended to be restrictive.  Any selectable marker gene may be used in the embodiments.  Suitable culture media and conditions for the host cells described above are well known in the art.  While intracellular expression may be advantageous in some respects, e.g. when certain bacteria are used as host cells, it is often preferred that the expression be extracellular or periplasmic.  In some embodiments, the Castellaniella defragrans LDHs mentioned herein include a pre-region / signal / leader sequence allowing the secretion of protease expressed in the culture medium or periplasm.  If desired, this pre-region may be replaced by a different pre-region or signal sequence, which substitution is suitably accomplished by substitution of the DNA sequences encoding the respective pre-regions.  The procedures used to link the DNA construct encoding a described polypeptide, promoter, terminator, and other elements, respectively, and to insert them into appropriate vectors containing the information necessary for replication, are well-known in the art. skilled person (see. for example, Sambrook et al. Molecular Cloning: A Laboratory Manual, supra).  In one embodiment, the cells described herein, comprising a DNA construct or an expression vector as defined above, are advantageously used in the recombinant production of a polypeptide as described herein.  The cell can be transformed with the DNA construct encoding the polypeptide as described herein, suitably, by integrating the DNA construct (in one or more copies) into the chromosome of the host.  This integration is generally considered an advantage because the DNA sequence is more likely to be stably stored in the cell.  The integration of DNA constructs into the host chromosome can be performed according to conventional methods, e.g. by homologous or heterologous recombination.  Alternatively, the cell can be transformed with an expression vector as described above in relation to the different types of host cells.  In some embodiments, a cell as described herein may be a cell of a higher organism such as a mammal or insect, a microbial cell, e.g. , a bacterium or fungus cell (including yeasts), or the like.  [0274] Without limitation, examples of suitable bacteria are Castellaniella defragrans, gram-positive bacteria such as Bacillus subtilis, Bacillus licheniformis, Bacillus lentus, Bacillus brevis, Bacillus stearothermophilus, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus circulans , Bacillus lautus, Bacillus megaterium, Bacillus thuringiensis or Streptomyces lividans or Streptomyces murinus, or gram-negative bacteria such as E.  al.  In one embodiment, the transformation of the bacterium can be effected for example by protoplast transformation or by using competent cells in a manner known per se.  In certain other embodiments, a yeast organism may be selected from Saccharomyces or Schizosaccharomyces species, e.g. , Saccharomyces cerevisiae.  The filamentous fungus may advantageously be part of an Aspergillus species, e.g. Aspergillus oryzae or Aspergillus congers.  Fungi cells can be transformed by a process including protoplast formation and protoplast transformation followed by regeneration of the cell wall 68 in a manner known per se.  Appropriate procedures for the transformation of fungal host cells are well known in the art.  In yet another set of embodiments, the present disclosure relates to a method of producing a polypeptide as described herein, said method comprising culturing a host cell as described above under conditions leading to the production of the polypeptide and the recovery of the polypeptide from the cells and / or the culture medium.  In some embodiments, the cells are grown under aerobic conditions.  In other embodiments, the cells are cultured under anaerobic conditions.  The medium used to culture the cells may be any conventional medium suitable for culturing the host cell in question and obtaining expression of the polypeptide as described herein.  Suitable media are commercially available or can be prepared according to published recipes (e.g. as described in the catalogs of the American Type Culture Collection).  [0278] Purification of polypeptides [0279] The polypeptide described herein and secreted from host cells can be appropriately recovered from the culture medium by well-known procedures, in addition to those described in the Examples section of this invention. description, comprising separating the cells from the medium by centrifugation or filtration, and precipitating the protein components of the medium by means of a salt such as ammonium sulfate followed by the use of chromatographic procedures such as chromatography-exchange chromatography. ions, affinity chromatography or others.  For example, fermentation, separation and concentration techniques are known in the art and conventional methods can be used to prepare the solution containing the concentrated polypeptide.  After fermentation, a fermentation broth is obtained and the microbial cells and various suspended solids comprising residual crude fermentation materials are removed by conventional separation techniques to obtain a polypeptide solution.  Filtration, centrifugation, microfiltration, rotary drum vacuum filtration followed by ultrafiltration, extraction or chromatography, or the like are generally used.  In some cases, it is desirable to concentrate the solution containing the polypeptide to optimize recovery because the use of unconcentrated solutions requires an incubation time to collect the precipitates containing the purified polypeptide.  The solution is concentrated using standard techniques until the desired level of enzyme is obtained.  The concentration of the solution containing the enzymatic polypeptide can be obtained by any of the techniques described above.  In one embodiment, rotary vacuum evaporation and / or ultrafiltration are used.  In one embodiment, a "precipitating agent" for purification purposes must be an effective compound for precipitating the polypeptide from the concentrated solution of enzymatic polypeptide in solid form, irrespective of its nature, namely crystalline, amorphous or a mixture of both.  Precipitation can be achieved using, for example, a metal halide precipitation agent.  The metal halide precipitation agents include: alkali metal chlorides, alkali metal bromides and mixtures of two or more of these metal halides.  The metal halide may be selected from the group consisting of sodium chloride, potassium chloride, sodium bromide, potassium bromide and mixtures of two or more of these metal halides.  Suitable metal halides include sodium chloride and potassium chloride, particularly sodium chloride, which can further be used as preservatives.  In one embodiment, a metal halide precipitation agent is used in an amount effective to precipitate the polypeptide.  Selection of at least one effective amount and an optimal amount of metal halide effective to cause precipitation of the enzymatic polypeptide as well as precipitation conditions for maximum recovery including incubation time, pH, temperature and the concentration of the polypeptide, will become apparent to those skilled in the art after routine tests.  In some embodiments, at least about 5% (A) w / v (w / v) to about 25% w / v metal halide is added to the concentrated enzyme polypeptide solution and usually at least 8% w / v metal halide is added to the concentrated enzyme polypeptide solution and usually at least 8% w / v. % w / v.  In some embodiments, no more than about 25 ° A) w / v of the metal halide is added to the concentrated solution of enzyme polypeptide and generally no more than about 20% w / v.  The optimum concentration of the metal halide precipitation agent will depend inter alia on the nature of the specific polypeptide and its concentration in the concentrated polypeptide solution.  Another embodiment for effecting the precipitation of the enzyme is to use organic compounds that can be added to the concentrated enzyme polypeptide solution.  The precipitation agent of the organic compound can include: 4-hydroxybenzoic acid, alkali metal salts of 4-hydroxybenzoic acid, alkyl esters of 4-hydroxybenzoic acid and mixtures of two or more of these compounds organic.  The addition of the precipitants of the organic compound can be carried out before, at the same time or after the addition of the metal halide precipitation agent and the addition of both the precipitants, the organic compound and the metal halide can be carried out sequentially or simultaneously.  In some embodiments, the organic compound precipitants are selected from the group consisting of 4-hydroxybenzoic acid alkali metal salts such as sodium or potassium salts and linear or branched alkyl esters. 4-hydroxybenzoic acid, the alkyl group containing 1 to 12 carbon atoms, and mixtures of two or more of these organic compounds.  In some embodiments, the precipitation agents of the organic compound may be, for example, linear or branched alkyl esters of 4-hydroxybenzoic acid, the alkyl group containing from 1 to 10 carbon atoms, and mixtures of two or more of these organic compounds.  In some embodiments, suitable organic compounds include linear alkyl esters of 4-hydroxybenzoic acid, alkyl group containing 1 to 6 carbon atoms, and mixtures of two or more of these organic compounds.  Methyl esters of 4-hydroxybenzic acid, propyl ester of 4-hydroxybenzic acid, butyl ester of 4-hydroxybenzoic acid, 4-hydroxybenzoic acid ethyl ester and mixtures of two or more of these organic compounds can also be used.  Additional organic compounds also include, but are not limited to, 4-hydroxybenzoic acid methyl ester (methyl-PARABENE) and 4-hydroxybenzoic acid propyl ester (propyl-PARABENE), which are also useful as preservatives. amylases.  [0287] In some embodiments, the addition of the organic compound precipitating agent provides the advantage of a high flexibility of the precipitation conditions with respect to pH, temperature, concentration of the polypeptide, the concentration of the precipitation agent and the incubation time.  In some embodiments, the organic compound precipitating agent is used in an amount effective to enhance the precipitation of the enzyme polypeptide by means of the metal halide precipitation agent.  Selection of at least one effective amount and an optimal amount of organic compound precipitating agent as well as precipitation conditions for maximum recovery including incubation time, pH, temperature and concentration of the enzymatic polypeptide will be readily apparent to those skilled in the art, in light of the present disclosure, after routine testing.  In some embodiments, at least about 0.01% w / v of the organic compound precipitating agent is added to the concentrated enzymatic polypeptide solution and generally at least about 0.02% w / v. .  In some embodiments, no more than about 0.3% w / v of the organic compound precipitating agent is added to the concentrated enzyme polypeptide solution and generally no more than about 0.2% w / v. v.  In some embodiments, the concentrated enzyme polypeptide solution containing the metal halide precipitation agent and in one aspect the organic compound precipitant is adjusted to a pH which will necessarily depend on the enzymatic polypeptide to be purified.  In some embodiments, the pH is adjusted to a level near the isoelectric point (pI) of the polypeptide.  For example, the pH can be adjusted in a range of about 2.5 pH units below pH to about 2.5 pH units above pH.  The incubation time necessary to obtain a precipitate of the purified enzymatic polypeptide depends on the nature of the specific enzyme polypeptide, the concentration of the enzyme and the specific precipitation agent (s) and its (their) concentration.  In some embodiments, the effective time for precipitating the enzymatic polypeptide is from about 1 to about 30 hours; usually it does not exceed about 25 hours.  In the presence of the organic compound precipitating agent, the incubation time can always be reduced to less than about 10 hours and in most cases even to about 6 hours.  In some embodiments, the temperature during the incubation is between about 4 ° C and about 50 ° C.  In some embodiments, the process is carried out at a temperature between about 10 ° C and about 45 ° C, and particularly between about 20 ° C and about 40 ° C.  The optimum temperature for inducing precipitation varies depending on the conditions of the solution and the enzymatic polypeptide or precipitation agent (s) used.  In some embodiments, the overall recovery of the purified enzymatic polypeptide precipitate and the efficiency with which the process is performed is enhanced by stirring the solution comprising the enzyme polypeptide, the added metal halide and the added organic compound.
[0005] In some embodiments, the stirring step is performed both during the addition of the metal halide and the organic compound, and during the subsequent incubation period. Suitable agitation methods include mechanical shaking or shaking, vigorous aeration or a similar technique. [0294] In some embodiments, after the incubation period, the purified enzyme polypeptide is then separated from the impurities and collected by conventional separation techniques, such as filtration, centrifugation, microfiltration, rotary vacuum filtration. , ultrafiltration, pressing filtration, transmembrane microfiltration, transmembrane flow microfiltration or the like. Transmembrane microfiltration can be a method used. In some embodiments, further purification of the purified enzymatic polypeptide precipitate can be achieved by washing the precipitate with water. For example, the purified enzymatic polypeptide precipitate is washed with water containing the metal halide precipitation agent, for example, with water containing the metal halide and organic compound precipitants. [0295] Compositions [0296] Certain embodiments relate to compositions comprising one or more described polypeptides, alone or in combination with a wild type 73 polypeptide of SEQ ID NO: 1 (with or without one of the first two Met, with or without a periplasmic label and with or without an additional C-terminal poly-His tag as described herein). In some embodiments, the composition comprises one or more polypeptides having improved activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene. In some embodiments, the composition comprises one or more polypeptides having enhanced enhanced specific activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene. In other embodiments, the composition comprises one or more polypeptides having improved activity and one or more polypeptides having increased specific activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene. In some embodiments, the composition may be composed of one or more polypeptides described, obtained (1) commercially; (2) cloned genes expressing said polypeptides; (3) complex broth (such as that resulting from the growth of a microbial strain or other host cell in media, wherein the strains / host cells secrete the described polypeptides into the media; (4) cell lysates strains / host cells cultured as in (3) and / or (5) any other material of the host cell expressing the described polypeptide Different polypeptides described in a composition can be obtained from different sources. [0298] In some embodiments, the composition comprises 3-buten-2-ol and one or more of the polypeptides described herein.In other embodiments, the composition further comprises a wild-type polypeptide of SEQ ID NO: 1 (with or without one of the first two Met, with or without a periplasmic label and with or without an additional C-terminal poly-His tag as described herein. [0299] In some embodiments, The position comprises 1,3-butadiene and one or more polypeptides described herein. In other embodiments, the composition further comprises a wild-type polypeptide of SEQ ID NO: 1 (with or without one of the first twoMet, with or without a periplasmic tag and with or without a poly-His tag C additional terminal as described herein). [0300] In some embodiments, the composition comprises a rubber product polymerized from 1,3-butadiene produced in the presence of a polypeptide as described herein. In some embodiments, the composition comprises a copolymer polymerized from 1,3-butadiene produced in the presence of a polypeptide as described herein. In some embodiments, the composition comprises a polymerized plastic product from 1,3-butadiene produced in the presence of a polypeptide as described herein. [0303] Antibodies capable of binding to a polypeptide of embodiments or relatives or fragments thereof which comprise at least one of the improved mutations / modifications described herein are also encompassed. Methods for the production of antibodies are well known in the art (see, for example, Harlow and Lane, (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY) and production manuals. newer antibodies recognized in the art. Methods of Use [0305] The polypeptides, nucleic acids, and compositions described herein can be used in many different applications. Some of these applications are described in the SUMMARY and / or the claims. An embodiment relates to a process for producing 1,3-butadiene comprising dehydration of 3-buten-2-ol to 1,3-butadiene in the presence of a polypeptide as described herein. Another embodiment relates to the use of a polypeptide as described herein in the preparation of a product, the product being polymerized from 1,3-butadiene produced in the presence of the polypeptide. In one embodiment, the product is a rubber product. In one embodiment, the product is a copolymer. In another embodiment, the product is a plastics material. Another embodiment relates to a method of constructing a described polypeptide, said method comprising (a) making modifications in the amino acid sequence, each of which is an insertion, deletion or substitution of a amino acid residue at one or more positions of SEQ ID NO: 1 (or SEQ ID NO: 1 without the periplasmic tag, or SEQ ID NO: 4 or 75), (b) the preparation of the polypeptide resulting from these modifications. (c) testing the 1,3-butadiene production activity of the polypeptide, (d) optionally repeating steps a) -c) recursively; and (e) selecting a polypeptide having improved 1,3-butadiene production activity relative to that of the wild-type polypeptide of SEQ ID NO: 1 (or SEQ ID NO: 1 without the periplasmic tag or SEQ ID NO: 4 or 5). All the claims in the list of claims are incorporated by reference in their entirety into the specification as additional embodiments.
[0006] EXAMPLES [0310] All the compositions and methods described and claimed herein can be produced and performed without unnecessary experimentation in light of the present disclosure and the knowledge of those skilled in the art.  In some cases, the compositions and methods of the present disclosure have been described in terms of embodiments; however, these embodiments are in no way intended to limit the scope of the claims and it will be apparent to those skilled in the art that variations may be applied to the compositions and / or methods and in the steps or sequence of steps of methods described herein without departing from the concept, spirit and scope of the invention.  More specifically, it will be apparent that certain components that are chemically and physiologically related may replace the components described herein while the same results or similar results will be obtained.  All such similar substitutes and modifications as will be apparent to those skilled in the art are considered to be in the spirit, scope and concept of the invention as defined in the appended claims.  1.  Enzymes [0311] Four enzymes were tested for the formation of the product of step b) of the following reaction: step a) isomerization and dehydration of the natural substrate linalool and step b) the dehydration of 3-buten-2-ol in 1,3-butadiene.  76 Linalool OH, buten Dehydration 1. . DH-H2O 'Myrcene LDH', Butene Isomerization, OH-1-120, Geraniol b) [0312] The four enzymes were: Castellaniella defragrans 1-linalol dehydratase / isomerase, EC 4. 2. 1. 127 abbreviated hereafter cdLD, Elizabethkingia meningoseptica 2-oleate hydratase and Streptococcus Pyogenes, EC 4. 2. 1. Abbreviated hereinafter em0H and sp0H, Thiocapsa roseopersicina 3-lycopene hydratase and Rubrivivax gelatinosus, EC 4. 2. 1. 131 abbreviated hereafter trLH and rgLH, and finally, 4-kievitone hydratase of Fusarium Phaseoli, EC 4. 2. 1. Abbreviated hereinafter fpKH).  Only the cdLD presented a repeatable activity for step b).  [0313] The amino acid sequence of C. linalool dehydratase.  defragrans (hereinafter referred to as cdLD) is available in public databases (accession number gi302064203 in the NCBI protein database) and has been reported by Brodkorb et al.  "Linalol dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes," Journal of Biological Chemistry, Vol 285 (40), pp 30436-30442.  The amino acid sequence used here is reproduced below.  It should be noted that, as described by Brodkorb et al. the sequence has the N-terminal signal MRFTLKTTAIVSAAALLAGFGPPPRAA (SEQ ID NO: 3) which is a bacterial periplasmic routing signal.  The protein used here also has an additional Met residue relative to the cdLD described in the NCBI database having Genbank accession number E1XUJ2. 1 77> gi13020642031embICBW30776. 11 precursor of linalool dehydratase-isomerase [Castellaniella defragrans] plus additional N-terminal methionine.  MMRFTLKTTAIVSAAALLAGFGPPPRAAELPPGRLATTEDYFAQQAKQAVTPDVMAQLAY MNYIDFISPFYSRGCSFEAWELKHTPQRVIKYSIAFYAYGLASVALIDPKLRALAGHDLD IAVSKMKCKRVWGDWEEDGFGTDPIEKENIMYKGHLNLMYGLYQLVTGSRRYEAEHAHLT RIIHDEIAANPFAGIVCEPDNYFVQCNSVAYLSLWVYDRLHGTDYRAATRAWLDFIQKDL IDPERGAFYLSYHPESGAVKPWISAYTTAWTLAMVHGMDPAFSERYYPRFKQTFVEVYDE GRKARVRETAGTDDADGGVGLASAFTLLLAREMGDQQLFDQLLNHLEPPAKPSIVSASLR YEHPGSLLFDELLFLAKVHAGFGALLRMPPPAAKLAGK SEQ1: amino acid sequence of CDLD wild type (SEQ ID NO: 1); SEQ ID NO: 1 without the first of the first two methionines is SEQ ID NO: 7.  The following DNA sequence (SEQ2) encodes the amino acid sequence of linalool dehydratase-isomerase listed above as SEQ 1.  It has a codon optimization for E.  neck i and is then cloned into the vector pARZ4 (a modified version of the vector pET29).  A C-terminal 6-HIS tag (SEQ ID NO: 10) is added to the sequence in the pARZ4 vector after a GS linker (Gly-Ser) and is included (in lowercase letters) in the sequence SEQ 2 below. below.  The total His tag is GSLEHHHHHH (SEQ ID NO: 6).  > Gi13020642031embICBW30776. 11 precursor linalool dehydratase isomerase [Castellaniella defragrans] atgATGCGTTTCACATTAAAGACCACCGCGATTGTTTCTGCCGCCGCGTTATTAGCGGGT TTTGGACCACCACCTCGTGCAGCAGAATTACCTCCCGGCCGCCTTGCCACAACCGAAGAT TATTTCGCACAACAAGCAAAACAAGCTGTAACCCCGGATGTTATGGCTCAACTCGCGTAC ATGAACTATATTGATTTCATTAGCCCCTTTTATTCACGTGGATGTTCATTCGAAGCATGG GAATTGAAACACACTCCGCAGCGCGTGATTAAATACTCCATTGCATTCTATGCTTATGGC TTGGCATCTGTAGCATTAATCGACCCTAAACTGCGCGCGCTCGCCGGCCACGACTTAGAT ATTGCAGTCTCAAAAATGAAATGTAAACGTGTATGGGGAGATTGGGAAGAAGATGGTTTT GGTACAGATCCGATTGAAAAAGAAAACATTATGTATAAAGGACATCTGAACCTTATGTAT GGTCTCTATCAACTTGTTACTGGATCGCGCCGTTACGAAGCTGAACACGCTCACCTCACC CGTATTATCCACGACGAAATTGCCGCCAACCCATTCGCCGGAATCGTTTGTGAACCAGAC 78 AACTATTTTGTACAATGCAACTCTGTGGCCTATTTAAGCCTTTGGGTCTACGATCGTTTA CATGGAACTGACTACCGTGCCGCAACTCGTGCCTGGCTGGATTTTATTCAAAAAGATCTG ATTGACCCCGAACGTGGAGCTTTCTATTTGTCCTATCATCCCGAATCTGGTGCCGTCAAA CCTTGGATCAGCGCATATACAACCGCTTGGACGTTAGCTATGGTGCATGGAATGGATCCT GCCTTTTCAGAACGTTATTATCCTCGTTTTAAACAAACGTTCGTCGAAGTCTATGATGAA GGCCGTAAAGCCCGCGTACGCGAAACTGCCGGAACCGACGACGCCGATGGTGGTGTGGGT TTAGCCTCTGCGTTCACACTTTTATTAGCCCGCGAAATGGGAGATCAACAACTCTTTGAC CAACTGCTGAATCATTTAGAACCCCCTGCCAAACCAAGCATCGTTTCTGCTAGCCTCCGC TACGAACACCCAGGCAGCCTCTTATTCGACGAACTGTTATTTCTTGCCAAAGTACATGCC GGATTTGGTGCTCTGTTACGTATGCCCCCTCCTGCCGCCAAATTAGCGGGCAAAGGTTCC ctcgagcaccaccaccaccaccactga SEQ 2: sequence optimized DNA encoding SEQ 1.  The sequence is optimized for the expression of E.  coli.  The start codon, the GS linker, and the His6 tag (SEQ ID NO: 10) are in lowercase letters (SEQ ID NO: 2) 2.  Expression and purification of proteins [0315] a.  Expression and purification of the per-cDLD in BL21 cells in the presence of the chaperone plasmids pKJE7, pGro7 and pTf16.  Plasmids expressing the chaperones were purchased from TaKaRa.  These were pG-KJE8 (expressing the chaperones dnaK-dnaJ-grpE groES-groEL), pGro7 (groES-groEL), pKJE7 (dnaK-dnaJ-grpE), pG-Tf2 (groESgroel-tig) and pTf16 (tig Periplasmic mutant cdLDs were expressed in BL21 cells with the plasmid pGro7 and purified by a His tag affinity resin.  Chemically competent BL21 cells carrying a pGro7 plasmid were transformed with the pARZ4 vector carrying the desired cdLD.  At day 1 of expression, overnight culture of 10 ml LB / KAN (50 μg / ml) with chloramphenicol (20 μg / ml) at 37 ° C was initiated in the evening.  At day 2, 500 ml of LB / KAN with chloramphenicol (20 μg / ml) was inoculated with 10 ml of culture overnight.  The culture was grown to a 0D600 nm of 0.6-0.8 at 37 ° C.  The cells were induced overnight with 500 μl of 1 M IPTG at 25 ° C.  The 500 ml culture was centrifuged at 9000xg at 20 ° C for 5 minutes.  The cells were resuspended in 6 ml of 50 mM Tris-HCl, pH 9/150 mM NaCl and stored at -20 ° C.  6 ml of cdLD pellet were lysed with lysozyme spatula tips, DNase I and 600 μl of 10% Bugbuster Protein Extract for 25 minutes at room temperature.  The lysed cells were centrifuged at 12,000 x g for 25 minutes at 5 ° C.  The supernatant was filtered with a 0.8 μm / 0.2 μm membrane.  The supernatant was loaded 3x onto a Ni-NTA column (1.25 ml bed volume).  The column was washed with 50 ml of 50 mM Tris-HCl, pH 9/150 mM NaCl and 50 ml of 50 mM Tris-HCl, pH 9/150 mM NaCl / 20 mM imidazole.  The cdLD was eluted with 10 ml of 50 mM Tris-HCl, pH 9/150 mM, NaCl / 250 mM imidazole.  10 ml of cdLD elution was degassed with argon for 30 minutes and 200 μl of 100 mM DTT was added to the elution.  10 ml of elution were concentrated to -2 ml in a Sartorius Vivaspin 15R centrifuge concentrator.  1.5 ml of concentrated cdLD was desalted with 2 ml of degassed 80 mM Tris-HCl, pH 9 in a Hi-Trap desalting column.  The 2 ml sample was covered with argon and stored at 4 ° C.  The cdLD was observed on an SDS gel with a molecular weight of -40 kDa.  The concentration of 2 ml of desalted cdLD was -1 mg / ml giving -2 mg per 500 ml of expression culture.  [0319] b.  Cyto-cdLD Expression and Purification in the Origami 2 (DE3) Strain [0320] The cytoplasmic cdLD was expressed in the Origami 2 strain (DE3) 20 with the following genotype: A (ara-leu) 7697 AlacX74 AphoA Pvull phoR araD139 AHPG galG galP rpsL Fliac + laclq pro] (DE3) gor522 :: Tn10 trx13 pLysS (CamR, StrR, TetR).  The chemically competent Origami 2 (DE3) cells bearing a pGro7 plasmid were transformed with pARZ4 (a deposited pET24 derivative) carrying the desired cdLD.  At day 1 of expression, cultures of 10 ml of LB / KAN (50 μg / ml) overnight at 37 ° C were initiated in the evening.  At day 2, 500 ml of LB / KAN were inoculated with 10 ml of culture overnight.  The culture was cultured up to OD600 nm 0.6-0.8 at 37 ° C.  The cells were induced overnight with 500 μl of 1 M IPTG at 25 ° C.  The 500 ml culture was centrifuged at 9000 x g, 20 ° C for 5 minutes.  Cells were resuspended in 6 ml of 50 mM Tris-HCl pH 9/150 mM NaCl and stored at -20 ° C.  [0322] 6 ml of cdLD pellet were lysed with lysozyme spatula tips, DNase I and 600 μl X Bugbuster 80 protein extraction reagent for 25 minutes at room temperature.  The lysed cells were centrifuged at 12,000 x g for 25 minutes at 5 ° C.  The supernatant was filtered with a 0.8 μm / 0.2 μm membrane.  The 3 x supernatant was loaded onto a Ni-NTA column (1.25 ml bed volume).  The column was washed with 50 ml of 50 mM Tris-HCl pH 9/150 mM NaCl and 50 ml of 50 mM Tris-HCl, pH 9/150 mM NaCl / 20 mM imidazole.  The cdLD was eluted with 10 ml of 50 mM Tris-HCl pH 9/150 mM NaCl / 250 mM imidazole.  10 ml of cdLD elution was degassed with argon for 30 minutes and 200 ul of 100 mM DTT was added to the elution.  10 ml of elution were concentrated to -2 ml in a Sartorius Vivaspin 15R centrifuge concentrator.  1.5 ml of concentrated cdLD was desalted with 2 ml of degassed 80 mM Tris-HCl pH 9 in a Hi-Trap desalting column.  The 2 ml sample was covered with argon and stored at 4 ° C.  It was observed on SDS gel that the cdLD exhibited a molecular weight of -40 kDa.  The concentration of 2 ml of desalinated cdLD was -1 mg / ml giving -2 mg per 500 ml of expression culture.  3.  Determination of butadiene in 1 ml for the linalool dehydration reaction Bacterial cells transformed with the appropriate constructs were taken from LB plates in 400 μl of LB medium containing 25 μg / ml of kanamycin in 96 well deep plates and incubated overnight at 37 ° C with vigorous shaking.  The following morning, 20 μl of this culture was inoculated overnight in 1 ml LB medium containing 25 μg / ml kanamycin in deep 96-well plates, shaken at 37 ° C for several hours.  When the cell density reached the appropriate level (OD of 0.6 to 600 nm), 0.5 μl of 1 M IPTG was added to each well (final concentration 500 μM).  Plates were incubated for 24 h at 25 ° C with vigorous shaking.  Then, 900 μl of cell culture was transferred into a crimp vial with 9 μl of 1.1 M 3-buten-2-ol (11 mM final concentration), sealed and incubated at room temperature for 72 h.  After incubation, the samples were analyzed in a Shimadzu GCMS-QP2010 Ultra column with Agilent HP PLOT / Q (0.32 mm, 15 m in length, 20 μm in diameter).  The program was as follows: the column was heated at 90 ° C for 1 min, then the temperature increased to 40 ° C per minute until reaching 200 ° C.  The ion source was heated to 230 ° C, interface to 180 ° C, admission to 250 ° C.  8 μl of the 81 head space of the crimp vial was injected in divided mode with a fractionation ratio of 2: 1.  The total head flow was 9 ml / min, septum purge flow rate of 3 ml / min and column flow rate at 2 ml / min.  Butadiene was detected at 2.26 min by monitoring ions with m / z 39, 50 and 54 in SIM mode.  The butadiene of each sample was compared to the wild-type cdLD enzyme present on each plate.  Relative activity was calculated as a ratio between the quantities of butadiene produced by a particular variant and the wild type enzyme.  This is the test of BL21 (DE3) which is the cell line for peri10 cdLD and cyto-cd L D.  4.  Assay for dehydration reaction of wild-type linalool (conversion of linalool to myrcene) Purified proteins were tested for their wild-type linalool dehydratase activity.  100 μl of purified protein was transferred into an eppendorf tube with 80 μl of degassed 80 mM Tris-HCl buffer (pH 9) as well as 20 μl of 100 mM linalool solution in DMSO.  Negative control reactions consisted of protein-free or linalool-free (substrate) tubes.  The tubes were stirred at room temperature for 1 h, then 200 μl of ethyl acetate was added.  This mixture was vortexed and centrifuged for 1 minute in a tabletop device.  The organic phase was transferred to a vial of DC and analyzed in a Shimadzu GCMS-QP2010 Ultra-Restek Rxi-624Sil column (0.32 mm, 60 m long, 1.8 μm in diameter).  The program was as follows: the column was heated at 100 ° C for 1 min, then the temperature increased at 50 ° C per minute to 280 ° C.  The injection temperature was 250 ° C.  8 μl of ethyl acetate solution was injected in a division-free mode.  The total head flow was 58 ml / min and the column flow rate was 1.86 ml / min.  Myrcene was detected at 5.50 min, linalool at 6.17 and geraniol at 6.96 by m / z ion control 69, 71 and 93 in SIM mode.  5.  Determination of crystalline structure A delta-BLAST search in the Protein Data Bank (PDB) protein sequence database revealed that the cdLD did not exhibit detectable homology with any sequence for which there was a structural model.  The crystalline structure of the cdLD was subsequently obtained by two private providers: Novalix, Illkirch-France and Emerald Bio, Bainbridge-WA.  Both companies followed the same general approach.  The protein expressed from a construct having a wild type cdLD sequence (SEQ 1) plus an HIS tag has been crystallized.  However, in the actual crystal structure obtained, the periplasmic signal / marker is cleaved, the first fully resolved residue is L29 (wild-type peri-cdLD numbering) and the last resolved residue is P390 (the HIS tag having no visible density.  It is the following sequence (SEQ ID NO: 11): LPPGRLATTEDYFAQQAKQAVTPDVMAQLAYMNYIDFISPFYSRGC SFEAWELKHTPQRVIKYSIAFYAYGLASVALIDPKLRALAGHDLDIAV SKMKCKRVWGDWEEDGFGTDPIEKENIMYKGHLNLMYGLYQLVT GSRRYEAEHAHLTRIIHDEIAANPFAGIVCEPDNYFVQCNSVAYLSL WVYDRLHGTDYRAATRAWLDFIQKDLIDPERGAFYLSYHPESGAV KPWISAYTTAWTLAMVHGMDPAFSERYYPRFKQTFVEVYDEGRKA RVRETAGTDDADGGVGLASAFTLLLAREMGDQQLFDQLLNHLEPP AKPSIVSASLRYEHPGSLLFDELLFLAKVHAGFGALLRMPP [0328] Three other additional structures having N-terminal deletions and C-termini have also been taken into account but none yielded the soluble protein in appreciable amounts: Construction 1 - deletion of G1u28-Thr36 residues and C-terminal cut at Arg387; construction 2 - deletion of residues G1u28-11e67; and construction 3 - deletion of residues G1u28- 11e67 and C-terminal cut at Arg387 (all relative to the wild type cdLD numbering of SEQ 1).  Their sequences are as follows: Del G1u28-Thr36 + C-ter cut at Arg387 (SEQ ID NO: 12)> giI3020642031embICBW30776. 11 precursor dehydratase isomerase linalool [Castellaniella defragrans] SIGNAL SEQ MMRFTLKTTAIVSAAALLAGFGPPPRAATEDYFAQQAKQAVTPDVM AQLAYMNYIDFISPFYSRGCSFEAWELKHTPQRVIKYSIAFYAYGLA SVALIDPKLRALAGHDLDIAVSKMKCKRVWGDWEEDGFGTDPIEKE NIMYKGHLNLMYGLYQLVTGSRRYEAEHAHLTRIIHDEIAANPFAGI VCEPDNYFVQCNSVAYLSLWVYDRLHGTDYRAATRAWLDFIQKDLI 83 DPERGAFYLSYHPESGAVKPWISAYTTAWTLAMVHGMDPAFSERY YPRFKQTFVEVYDEGRKARVRETAGTDDADGGVGLASAFTLLLAR EMGDQQLFDQLLNHLEPPAKPSIVSASLRYEHPGSLLFDELLFLAKV HAGFGALLRGSLEHHHHHH [0330] Del G1u28-1Ieu67 (SEQ ID NO: 13)> giI3020642031embICBW30776. 11 precursor dehydratase isomerase linalool [Castellaniella defragrans] SIGNAL SEQ MMRFTLKTTAIVSAAALLAGFGPPPRAASPFYSRGCSFEAWELKHT PQRVIKYSIAFYAYGLASVALIDPKLRALAGHDLDIAVSKMKCKRVW GDWEEDGFGTDPIEKENIMYKGHLNLMYGLYQLVTGSRRYEAEHA HLTRIIHDEIAANPFAGIVCEPDNYFVQCNSVAYLSLWVYDRLHGTD YRAATRAWLDFIQKDLIDPERGAFYLSYHPESGAVKPWISAYTTAW TLAMVHGMDPAFSERYYPRFKQTFVEVYDEGRKARVRETAGTDD ADGGVGLASAFTLLLAREMGDQQLFDQLLNHLEPPAKPSIVSASLR YEHPGSLLFDELLFLAKVHAGFGALLRMPPPAAKLAGKGSLEHHHH HH [0331] Del G1u28-1Ieu67 + cut C-ter at Arg387 (SEQ ID NO: 14)> giI3020642031embICBW30776. 11 precursor dehydratase isomerase linalool [Castellaniella defragrans] SIGNAL SEQ MMRFTLKTTAIVSAAALLAGFGPPPRAASPFYSRGCSFEAWELKHT PQRVIKYSIAFYAYGLASVALIDPKLRALAGHDLDIAVSKMKCKRVW GDWEEDGFGTDPIEKENIMYKGHLNLMYGLYQLVTGSRRYEAEHA HLTRIIHDEIAANPFAGIVCEPDNYFVQCNSVAYLSLWVYDRLHGTD YRAATRAWLDFIQKDLIDPERGAFYLSYHPESGAVKPWISAYTTAW TLAMVHGMDPAFSERYYPRFKQTFVEVYDEGRKARVRETAGTDD ADGGVGLASAFTLLLAREMGDQQLFDQLLNHLEPPAKPSIVSASLR YEHPGSLLFDELLFLAKVHAGFGALLRGSLEHHHHHH [0332] All constructs contain the periplasmic N-terminal tag.  Ni-NTA expression and purification for the Novalix crystals proceeded as follows.  CdLD cultures were performed in BL21 (DE3) bacteria in 1 L of Power Broth medium.  Induction with IPTG was performed at 18 ° C overnight.  After centrifugation, the pellets were resuspended in 200 ml of lysis buffer (Tris pH 8, 20 mM, 500 mM NaCl, 10% glycerol, Imidazole pH 8, 10 mM, 1% Chaps, TCEP 1 mM) for a 6 L culture and treated with ultrasound.  After centrifugation at 53,000 g, the soluble extract was incubated with about 2 ml of Talon beads overnight.  The column was washed with a volume of 5 columns of lysis buffer and elution was carried out in one step with elution buffer (Tris pH 8, 20 mM, 500 mM NaCl, glycerol 10 ° / (:) imidazole pH 8, 250 mM, 1 mM Chaps, 1 mM TCEP).  Then, the sample was applied to a SEC column (Hiload 16/60 S75) pre-equilibrated with SEC buffer (Tris, 20 mM pH 8, 150 mM NaCl, 5% glycerol).  Purification gave an average of 2 mg of pure cdLD protein per 6 L of culture.  The protein was then concentrated to 6 mg / ml in SEC buffer prior to crystallization tests.  In total, 960 crystallization conditions were tested.  The cdLD crystals used for the determination of the structure were obtained under a Morpheus H2 screening condition (P8000 10 ° / (:), ethylene glycol 20 ° / (:), 0.02 M Na-1-glutamate, dl 0.02M alanine, 0.02M glycine, 0.02M dl-lysine HCl, 0.02M dyserine) at 295 ° K.  Crystals appeared in a few days and were very fine and delicate to handle.  With the ethylene glycol in the mother liquor, crystals could be removed and frozen directly in liquid nitrogen. The conditions for the expression and purification of the Emerald crystals were as follows.  The plasmid cdLD provided by Arzeda has been expressed as secreted protein in the periplasmic space.  The fermenation conditions were as follows: E. coli culture  neck carrying the plasmid pARZ_cdLD (expressing cdLD with the sequence shown in the table below, SEQ ID NO: 9) at the 8 L scale in 1 L stirred flasks of LB medium, induced at a OD -0.600 with 1 mM IPTG and grown overnight at 25 ° C.  target protein sequencing CDLD this AA MMRFTLKTTAIVSAAALLAGFGPPPRAAELPPGRLATTEDYFAQQAKQAVTPDVMA QLAYMNYIDFISPFYSRGCSFEAWELKHTPQRVIKYSIAFYAYGLASVALIDPKLRALAG HDLDIAVSKMKCKRVWGDWEEDGFGTDPIEKENIMYKGHLNLMYGLYQLVTGSRR YEAEHAHLTRIIHDEIAANPFAGIVCEPDNYFVQCNSVAYLSLWVYDRLHGTDYRAAT RAWLDFIQKDLIDPERGAFYLSYHPESGAVKPWISAYTTAWTLAMVHGMDPAFSER YYPRFKQTFVEVYDEGRKARVRETAGTDDADGGVGLASAFTLLLAREMGDQQLFDQ LLNHLEPPAKPSIVSASLRYEHPGSLLFDELLFLAKVHAGFGALLRMPPPAAKLAGKHH HHHH color code marker His bold / underlined characters, secretion signal in bold 85 3033 172 [0334] The slurry of E.  was / was delivered on ice and the cells were ruptured by light osmotic shock to release the periplasmic proteins.  A detailed protein purification protocol is presented below.  Briefly, the protein was purified by Ni-IMAC chromatography using the C-terminal polyhistidine chromatographic tag followed by exclusion-diffusion chromatography.  The purification yields were about 1 mg per liter of E.  silent /.  [0335] Initiation with 8 L of E.  Coil /: Release Light Osmotic Shock Buffer (MOSB): Tris / 200 mM HCl, pH 7.5, periplasmic 20 ° A (w / v) sucrose, one complete tablet of free protease inhibitor without EDTA (ice-cooled ).  1.  The sample pellets are suspended in 800 ml (10% of culture volume) of ice-cold MOSB with 400 mg of lysozyme added to the buffer just prior to use.  The sample is stirred slightly on ice for 20 minutes.  2.  After 20 minutes, 800 ml of ice cold diH 2 O was added to the sample and stirred slightly for a further 20 minutes.  3.  The samples are agglomerated by centrifugation at 5000 rpm for 30 min at 4 ° C.  4.  The supernatant is removed, filtered in a 0.2 μm flask filter and purified by Ni-NTA affinity chromatography.  Purification of Proteins: Purification Step 1 [0337] All purification steps are performed at 4 ° C.  The AKTA systems are rinsed thoroughly with water and then buffers before the initiation of the purification.  Chromatography type Ni I Column type used HiTrap Ni chelating Quantity of columns used 1 x 5 ml New or regenerated New 50 mM Tris buffer, pH 9, 0.15 M NaCl, 20 mM imidazole.  prepared on 19/02/2013.  50 mM Tris buffer, pH 9, 0.15 M NaCl, 250 mM imidazole.  prepared on 19/02/2013.  Wash buffer 50 mM Tris, pH 9, 0.15 M NaCl.  Prepared on 19/02/2013 Column balancing 4 HP A, 4 HP B, 4 HP A AKTA system used BB-AKTA 2 Load volume and flow 1.6 I, 1.5 ml / min Washing volume and flow 50 ml, 2 ml / min Elution gradient, start and fraction size 0-60 ° AB in 120 minutes, 1 ml / min, fractions 5 ml.  Comments N / A SDS-PAGE analysis 4 to 12 ° A MOPS SDS-PAGE denatured at 95 ° A for 5 minutes with 4 x SDS loading dye containing 2-mercaptoethanol.  Protein purification: concentration, step 1 (concentration objective: 15 mg / mi) Type of concentrator, MWCO, centrifugation speed and duration Vivaspin 20 PES, 10 kDa MWCO, 5000 to 6500 RCF, 10 to 20 minutes d range Initial volume concentration (Nanodrop-1000) and 0.3 mg / ml, 45 ml Concentration final volume (Nanodrop-1000) and 5.05 mg / ml, 2.2 ml Purification of proteins: purification, step 2 Type of chromatography SEC Column type used Sephacryl S-100 16/60 Quantity of columns used 1 x 120 ml 10 mM SEC Tris buffer, pH 9.0, 350 mM NaCl, 2 mM DTT.  Prepared on 20/02/2013.  Column balancing Buffer SEC 100%, 240 minutes at 0.5 ml / min AKTA system used BB-AKTA 2 Injection volume and flow 2.2 ml, 0.5 ml / min Number of injections 1 x 2.2 ml Fraction size 3 ml Comments N / A SDS-PAGE analysis 4 to 12 ° A MOPS SDS-PAGE denatured at 95 ° A for 5 minutes with 4 x SDS-loading dye containing 2-mercaptoethanol.  87 SDSPAGE Analysis Conditions Reduced Number of Aliquots, Volume, 8 x 100 μl, 1 x 50 μl to 10.28 mg / mi Concentration Final Protein Yield 8.74 mg Final Buffer Tris 10 mM, pH 9.0 350 mM NaCl, 2 mM DTT.  [0340] 3) Crystal Growth and Handling: Crystals for the determination of the cdLD structure were obtained using the vapor diffusion method with 400 nL of protein solution (9.06 mg cdLD) / mL in 10 mM Tris, pH 9.0, 350 mM NaCl, 2 mM DTT) mixed with 400 nL of crystallization solution on a reservoir of -40 μl of crystallization solution.  Crystallization conditions suitable for crystal growth were determined by testing 576 random hollow matrix conditions of various commercially available crystallization screen systems.  Small crystals were obtained from the Morpheus commercial screening system (Molecular Dimensions, Newmarket UK).  Morpheus screening uses complex mixtures of buffer precipitation agents and additives.  A description of the screening can be found at: www. moleculardimensions. com / applications / upload / MD1- 47 / 020Morpheus% C2 ° / 0AE. pdf.  Based on these initial crystallization elements, an optimization screen was created using various concentrations of Morpheus buffers.  The crystal from which the data was obtained was grown from the following components: 39.55% (v / v) of "EDO_P8K" Morpheus, a mixture of ethylene glycol and PEG 8000 10 ° A) ( v / v) amino acids Morpheus, a mixture of L-Naglutamate; alanine (racemic); glycine; lysine HCI (racemic); serine (racemic) 6.12 ° A) (v / v) MES 1.0 M and 3.88% (v / v) 1.0 M imidazole; pH 6.5 In addition, the crystallization drop that gave the crystal used for data collection also contained 0.05% (v / v) 3-buten-2-ol.  The crystallization solution was a "direct cryo", that is to say a solution that would be subjected to a vitreous transition to a solid during a rapid cooling in liquid nitrogen. and therefore, no additional cryoprotectant was required to freeze the crystal for data collection.  The crystal was transferred to a crystal mounting loop and subjected to flash cooling by being immersed in liquid nitrogen.  All crystal growth took place in a temperature controlled room at 16 ° C.  X-ray diffraction data collection: The data was collected via remote access to the Advanced Photon Source in Argonne, IL on the 21-ID-D beamline on April 18, 2013 using a detector. MarMosaic 300 CCD.  Data was processed and scaled using XDS / XSCALE.  Data collection, scaling and refinement statistics are summarized in the following table: Parameters Global (highest hull) APS source of radiation 21-ID-D Collection date 18 April 2013, 8.4) 1 , 0 ° Frames 250 Distance 300 mm Wavelength 0.93005 A crystal ID 244270a7, palet ID lab8-4 Space group P21 Unit cell a = 88.70, b = 111.22, c = 120.42; a = 90.0, [3 = 102.72, y = 90.0 Resolution 2.60 A (2.67 A - 2.60 A) 1/0 16.17 (2.71) Completeness 99.8 ° A (99.9%) Rmerge 7.4% (51.4 ° A) Reflections (unique) 284619 (70173) Mutiplicity 4.06 Refinement Statistics Rcrist.  17.20% RI 22.20% MSD bonds 0.011 MSD angles 1.430 Average B factor 28.64 89 3033 172 Determination of Emerald crystal structure: The cdLD structure was resolved by molecular replacement using the Phaser program as implemented in the suite of CCP4 programs with a protein model representing a preliminary structure of the same target created by Novalix as a search pattern.  The initial MR solution was refined using the Refmac5 program.  The cdLD model was then refined using alternative hand-reset cycles in Coot with restricted refinement with Refmac5.  The final R / R ratio of the model was 17.20% / 22.20 (Yo.  Since no structural homolog is known for cdLD, phase determination can not be performed by molecular replacement, however, either isomorphous or MAD / SAD replacement is required.  For Novalix crystals, the isomorphous replacement was unsuccessful, therefore, Sel-met MAD was chosen for the Novalix crystals.  In order to obtain a Se-met-labeled cdLD, cultures were performed in M9 medium supplemented with Se-met 80 mg / ml in strain B834.  An initial culture was performed in LB medium and was used for inoculation of the M9 culture.  Then, induction with IPTG was performed at 18 ° C overnight.  A purification protocol similar to the native cdLD was performed for the Se-met labeled protein.  An average purification yield gave about 2 mg of labeled cdLD per 12 L of M9 culture.  The crystals used for the diffraction of MAD were obtained under the same conditions as those of the native protein.  Se-met-labeled and native protein crystals are part of the same P21 space group but with 2 different cells.  CdLD Se-mα crystals diffract only at a resolution of 3.7 Å over a 2.5 A resolution for a native cdLD crystal.  After identification and refinement of Se atom positions, a first cdLD model was built at 3.7 A resolution with CCP4 suite software and ShelX.  The phases were then developed at a resolution of 2.5 A by molecular replacement in a native data group.  Table 1: synchrotron data of the native CV32 protein Native cdLD protein CV32 data group Proxima 1 X-ray source (SOLEIL) Wavelength (A) 0.98011 Detector distance 439.7 mm Oscillation 0.2 ° Exposure time 0.2 seconds Table 2: Crystallographic data Data group CV32 Resolution 48.16-2.54 (last shell) (A) (2.69-2.54) Space group P2 (1) a = 133 , 18 A b = 110.83A c = 162.20 A Unit cell a = 90.00 ° f3 = 107.157 ° y = 90.00 ° Single reflections 154892 Integrity (last shell) (° / 0) 99.0% ( 96.10%) Redundancy 3.4 II E (I) (last hull) 13.84 (2.08) Rsy, (I) (last hull) (° / 0) 7.71% (58.60%) Wilson plot B 48.08 A2 [0346] Crystal coordinates are provided in Appendix 1 for Novalix Crystal and Appendix 2 for Emerald Crystal.  The statistics for the resolved structure of Novalix crystals are shown in Tables 1 and 2 6.  General characteristics of the apocd LD high-resolution 3D model Part I: Novalix: cdLD adopts a pentameric arrangement associated with an axial symmetry of factor 5 in the asymmetric unit (chain marked A to E).  Each monomer adopts barrel folding 0/0 (6), a generally unusual folding that can be seen in FIGURE 1.  In the crystalline structure 91, a disulfide bridge is formed between Cys74 and Cys127 of each subunit (crystal structure numbering).  A structural homology search using the DALI program yielded various structural counterparts.  A structural alignment between the cdLD monomer and some of the DALI alignment successes revealed that the enzymes that are structurally homologous to cdLD all have their active sites at the "top" of the barrel, the catalytic residues being supported by the internal helices that coat. the inside of the barrel (propellers 4, 7, 9, 11, 13, 14) and the loops connecting these propellers are the external propellers of the barrel.  Consistent with other similar folding enzymes, cdLD shows a marked slit in this same region while the rest of the subunit is fully exposed to the solvent in a tightly compact manner.  Therefore, we hypothesized that the likely position of the active site of the cdLD responsible for the observed catalytic activity is located in this region.  Unlike most cdLD structural counterparts, this hypothetical active site is formed at the interface between subunits, for example, A and B in FIGURE 1.  The 62-77 (crystal structure numbering) loop of subunit B protrudes and closes the pocket formed by the top of the sub-unit A barrel, see FIGURE 2.  [0349] Below is presented the mapping of amino acid residues (in the wild-type peri-cdLD numbering) for each secondary structural element.  A secondary structure assignment was made using the DSSP software (note that the term "propellers" here includes a, 310 and 7).  The loops are not included because they actually constitute all the remaining positions.  See also FIGURE 3.  92 3033 172 Helix Residues from beginning to end (peri-cdLD numbering [SEQ 1]) H1 37-41 H2 43-46 H3 51-61 H4 77-82 H5 86-106 H6 108-125 H7 128-131 H8 133- 136 H9 149-165 H10 172-188 H11 203-220 H12 228-236 H13 264-274 H14 279-293 If 294-296 H15 298-300 S2 303-305 H16 321-331 H17 335-345 S3 351-353 S4 358-360 H18 368-377 H19 381-385 [0350] Table 3: Residue numbers for each secondary structure element (H helices and S strand) of cdLD, based on the high resolution crystalline structure.  Secondary structure assignments were obtained with DSSP 2. 2. 1.  The propeller annotations include CI, 310 and O propellers.  The 5 strands correspond to the residues in the extended conformation, whether or not they actually form strands 0.  [0351] Part II: Emerald Crystals The asymmetric crystal unit cdLD is a pentamer having an axial symmetry of factor 5.  Each individual subunit forms a head-tail interaction with a neighboring subunit where a loop around Tyr70 protrudes into a cavity in the center of the barrel of the 6-alpha helix of the cdLD 5 monomer (top figure).  At this interface is a narrow pocket,> 10A deep, which includes the hypothetical active site (Figure 16).  During the refinement of the Emerald crystal structure, a significant electron density characteristic was observed in all five subunits between Cys196 residues (wild type cdLDs but Cys197 for wild type cdLDs). with an additional N-terminal amino acid) and Cys205 (wild-type cdLD, but Cys206 for wild type cdLDs with an additional N-terminal amino acid).  The shape of the electron density characteristic and the chemical coordination around the site corresponded to a metal ion bond.  The metal ion was supposed to be zinc but the real identity is unknown.  No zinc or other divalent metal was present in the crystallization solution, however, a metal ion could have been transported during the purification or be present as a trace contaminant of the glass material.  Additional features of low electron density (green mesh in Figure 17) have been observed but not modeled.  The electron density characteristics observed were not consistent with those of 3-buten-2-ol or individual water molecules.  One explanation is that 3-buten-2-ol and / or other crystallization components may have been present at low occupancy and / or multiple conformations in the hypothetical active site slot, preventing appearance of a clear electronic density.  7.  CdLD active site mutants based on Novalix crystal data [0354] Based on the visual analysis of the hypothetical active site, a list of polar groups lining the active site pocket was chosen to further perform mutagenesis. to evaluate their effect on catalytic activity for the wild-type reaction catalyzed natively by cdLD.  The list of candidate active site residues and proposed mutations that are expected to affect catalytic activity is shown in Table 4 below.  Periplasmic cdLD in BL21 with PGro7 cytoplasmic cdLD in Origami2 (DE3) periplasmic cdLD in BL21 with PGro7 cytoplasmic cdLD in Origami2 (DE3) Mutant Y99F Protein Protein activity on weak PAGE Activity with linalol Mutant H115D Protein on PAGE Activity with linalool Protein Activity with linalol Y99A Y92F Y92A e on with low par- H115A E198Q E198A weak 1 on par- Y71F PAGE 1 linalool +: tielle D65N D65A 5+ I or PAGE tielle Y71A + weak YES partial C206S 1 YES weak 1 Y266F low par- C206A C197S ND I YES Y266A weak C197A 1 YES Q205L low 1 par- WT peri WT cyto Q205A: partial M151L YES M151K M151A + 1 partial [0355] Table 4.  Hypothetical catalytic residues, proposed catalytic activity of knock-out mutations and impact on protein expression (peri-cdLD or cyto-cdLD) and catalytic activity for dehydration of linalool to myrcene.  Each mutant was expressed and tested to determine its wild-type linalool dehydratase activity (Example 4).  From these results, it is expected that the following residues are candidate catalytic residues: CYS197, CYS206, ASP65 and GLU198.  These are the only residues for which cdLD was expressed and no catalytic activity compared to dehydration of linalool was observed.  8.  mutant cdLDs result in increased butadiene production [0357] a.  Activity in cell cultures (i.e., in vivo activity) Approximately 400 mutant cDLDs and sequence homologs were screened for their activity with 3B20 as a substrate.  See Appendix 3 for the 95 sequences.  All constructs were made in plasmid pARZcdLD.  This plasmid is derived from the PET-29a vector, the cdLD gene having been cloned between the NdeI and XhoI restriction sites.  The expression vector contains the T7 promoter, a lac operator and an N-terminal His tag.  The cdLD variants described here were constructed at Gene9 Inc.  (Cambridge, MA) with the deposited processes of this company.  All genes were synthesized with the following overhangs: CTCTTCTTAACTTTAAGAAGGAGATATACAT (upstream) and CTCGAGCATCATCATCATCATCATCACTCACTGAGATCCGGCTGCTAACAAAGCCCGGA AGAG (downstream) (SEQ ID NO: 15-16, respectively).  Ten microliters of each cdLD variant were separated by Earl restriction enzyme (New England Biolabs) and purified by a Qiagen QiaQuik PCR purification kit according to the manufacturer's protocol.  Then, all the constructs were cloned into pARZ-4, which is identical to the pARZ-cdLD plasmid except that the cdLD gene is replaced by a filler fragment.  The pARZ-4 backbone was amplified with the following primers.  G i bsV4 Rev (GTATATCTCCTTCTTAAAGTTA) and G i bsV3for (TGAGATCCGGCTGCTAACAAAGC) (SEQ ID NO: 17-18, respectively).  Each PCR amplification reaction contained 30 pmol of each primer and 100 ng of dnaE template.  Amplifications were performed using Pfu Ultra II Hotstart DNA polymerase (Agilent cat # 600850-51).  The PCR reaction (20 μl) was initially heated at 95 ° C for 2.5 min followed by 30 denaturation cycles at 94 ° C for 15 sec. annealing at 55 ° C for 15 sec.  and elongation at 72 ° C for 5 min.  After amplification, the PCR fragment was gel purified by the QIAGENO gel band purification kit according to the manufacturer's protocol.  1 μl of the amplified vector (about 0.05 pmoles) was mixed with 4 μl (approx.  0.3 pmol) of cdLD variant and 5 μl of Gibson Assembly 2 mixture (New England Biolabs, Cat # M5510AA) and incubated for 1 h at 50 ° C.  After incubation, each mixture was diluted in sterile water (4 times) and transformed into XL1Blue competent cells (Agilent) according to the manufacturer's protocol.  Transformed cells were plated on LB plates containing 25 μg / ml kanamycin and incubated overnight at 37 ° C.  The next day, the colonies were tested for the presence of the PCR insert of the colonies.  The colonies were removed and resuspended in 20 μl of sterile 0.9% sodium chloride solution.  One μl of this solution was transferred to the PCR tube and amplified with Taq polymerase (New England Biolabs, cat # M0482S) and 30 pmoles of primers P1 (ATAGGCGCCAGCAACCGCAC) and P2 (GCAGCAGCCAACTCAGCTTC) (SEQ ID NO. 19-20, respectively).  Each PCR reaction (20 μL) was heated initially at 95 ° C for 2.5 min followed by 30 denaturation cycles at 94 ° C for 15 sec. annealing at 55 ° C for 15 sec.  and elongation at 72 ° C for 1 min.  The amplification products were visualized by agarose electrophoresis.  Clones with the correct inserts were inoculated into culture tubes containing 5 ml LB and 25 μg / ml kanamycin and incubated overnight at 37 ° C.  The following day, the constructs were purified by a Qiagen miniprep kit and transformed into BL21 competent cells (DE3) (purchased from Invitrogen).  These cells were plated on LB plates containing 25 μg / ml kanamycin and incubated overnight at 37 ° C.  Each mutant was tested with the 1 ml test of butadiene (Example 3).
[0007] Clones that produced butadiene at levels comparable to or greater than those of the wild type enzyme were re-cultured in multiple replicates and re-tested using the same assay with 1 ml of butadiene. The most interesting variants were retransformed into BL21 cells (DE3) to avoid the potential influence of somatic mutations of the host and also tested again in a 1 ml test of butadiene. Some of the results are presented in FIGURE 4. First, four clones showed a marked improvement in butadiene production in vivo compared to the wild-type peri-cdLD enzyme. These were clones 91 (V1231, V2041, M274F, V275I), 92 (V1231, V2041, M274F, V275I, F382W), clone 1 (A324L) and clone 31 (R360Y). Clone 90 (V1231, V204I, V275I) differed from clone 91 by a single mutation (M274F), but did not result in an increase in butadiene production. [0360] An additional group of mutants was tested in the same test. the results are shown in FIG. 5. Mutant A324L which was part of clone 1 above, was again found to increase the catalytic activity in this test with 1 mL of butadiene. It has also been found that the A324E mutation has a similar activity. In contrast, the A324C mutation was found to have no effect on butadiene production. Other mutants which exhibited increased activity were: L328V, S366V, S366C and L212F. The highest increase was obtained with the mutant S366V. [0361] Several additional mutations were introduced into each of these improved mutants to try to further increase their activity. The results are shown in Figures 6-8. As can be seen in FIGURE 6, three different clones with identical double mutations A324L and S366G exhibited increased production of butadiene relative to their parent (A324L) and wild-type. The M274F mutant was a less effective butadiene producer than the wild type. The addition of F96L (double mutant M274F and F96L) resulted in an increase in butadiene production (FIGURE 7). The addition of mutations to S366V (FIGURE 8) and V275I (FIGURE 9) did not improve butadiene production relative to the rate obtained with the wild-type. Addition of the L328V mutation on F328W (double mutant F382W-L328V) appeared to enhance butadiene production (FIGURE 10). [0362] b. Activity in Purified Samples Four cdLD variants were purified with the standard His tag purification procedure described in Example 2: wild type, clone 91, clone 30 and clone31. Proteins were diluted to the same concentration. 250 μl of purified protein solution was transferred into a crimp vial with 2.5 μl of 1.1 M 3-buten-2-ol (11 mM final concentration), sealed and incubated at room temperature for 72 h. After incubation, the samples were analyzed by a Shimadzu GCMS-QP2010 Ultra with Agilent HP PLOT / Q column (0.32mm, 15m in length, 20μm diameter) as described above for the test. 1 ml of butadiene. The results are shown in FIGURE 11. None of the variants showed an improvement in butadiene production when tested in this assay. [0364] Another purification protocol was also used. From a fairly fresh LB plate containing the desired transforming clone, a colony (or a small scratch sample) was taken to inoculate 10 to 50 mL of LB supplemented with the relevant antibiotic and the pre-culture was incubated. overnight at 37 ° C, 230 rpm. The next morning, the self-induction TB medium (Merck / Product code: 71491-5) was prepared by mixing 60 g of TB / L supplemented with 10 ml of glycerol / L of TB and place in the microwave for 3 + 2 minutes at full power. The TB is allowed to cool under the hood before use and distribute in sterile vials. Then the pre-culture incubated overnight is centrifuged and the supernatant is removed. The preculture is resuspended in 1 to 5 mL of freshly prepared TB medium and used to inoculate 100 to 500 mL of TB dispensed into sterile vials, supplemented with the appropriate antibiotic. The inoculated flasks are incubated at 28-30 ° C for at least 20 h at 230 rpm. The main culture is centrifuged at least at 3000 g / 20 min / 4 ° C and the pellets are used immediately. The pellets are resuspended in 10 to 20 ml of buffer A (= 50 mM Tris + 150 mM NaCl + 40 mM Imidazole + 5% glycerol - pH 8.5). The cells are resuspended and then sonicated on ice for 5 minutes at 35-40% amplitude with sonication pulses of 5 "ON and 15" OFF. The sonicated cells are centrifuged for at least 15500 g, 20 min at 4 ° C. The supernatant containing the soluble fraction of the proteins was recovered and used for the purification of the Histrap protein. The filtered soluble fraction of the proteins obtained after extraction of the proteins by sonication was used for the purification of the His marker protein. A 1 mL His-trap column (EC Healthcare / Product Code: 17-5319-01) was equilibrated with 5- column volumes (VC) using Buffer A *. The soluble fraction of the proteins was manually loaded onto the His-trap column using a syringe and 5-10 VC of buffer A was used to wash the His-trap column. 5-10 .mu.C Buffer B ** was used to directly elute the His marker protein on a 4 or 20 mL centrifugation filtration unit (VWR / Product Code: 512-2850) with a corresponding threshold (5 kD). ). The centrifugation unit was used at 3500 g / 5 ° C to a volume less than 400 μl of concentrate. About 3 mL of buffer C was added to the concentrate and the centrifugation unit was used again at 3500 g / 5 ° C to a volume less than 400 μL. This step was performed to remove most of the imidazole used in buffer B to elute the His tag. The concentrate was recovered and depending on the working concentration (= 2 mg / mL), buffer C was used to supplement the desired volume. The concentration was verified using a Nanodrop spectrophotometer. Buffer A = 50 mM Tris + 150 mM NaCl + 40 mM Imidazole + 5% (v / v) glycerol - pH 8.5 [0370] ** Buffer B = buffer A + 400 mM imidazole pH 8.5 [0371] Buffer C = Imidazole-free buffer A-pH 8.5 The purified proteins were used for the butadiene assay. A 1 mL reaction mixture consisting of 2 mg / mL of each enzyme purified with 10 mM 3-buten-2-ol or 3-methyl-3-buten-2-ol for the biosynthesis of 1,3-butadiene or isoprene respectively, was prepared in 1.7 mL of crimped glass vial. The flasks were incubated for at least 48 h at 30 ° C, 170 rpm. Butadiene and isoprene were analyzed by headspace GC-MS using an authentic standard to determine a standard quantization curve. . The results are shown in FIG.
[0008] 12A. Mutants F382W / L328V; F382W / L328V / I187M; and A324L / S366G all exhibited increased dehydration activity of 3-buten-2-ol to butadiene, relative to wild-type cdLD. [0374] The same three mutants purified in the same way were also tested for their ability to produce isoprene from 3-methyl-3-buten-2-ol. [0375] A 1 mL reaction mixture consisting of 2 mg / mL of each enzyme purified with 10 mM 3-methyl-3-buten-2-ol for the biosynthesis of isoprene was prepared in a glass vial. set with 1.7 mL. The flasks were incubated for at least 48 h at 30 ° C, 170 rpm. Isoprene was analyzed by headspace GC-MS using an authentic standard to determine a standard quantization curve. The results are shown in FIG.
[0009] 12B. Again, all mutants F382W / L328V; F382W / L328V / I187M; and A324L / S366G exhibited increased isoprene production activity compared to wild-type cdLDs. 9. Further characterization of the activity of clone 91 [0377] a. Study of the effect of individual mutations in clone 91 [0378] In order to analyze mutations of clone 91 that contribute to increased butadiene production, each of the mutations was individually created in wild-type cdLD. Similarly, each mutation was removed individually from clone 91. The choice to focus on the 91 was based on the 100 3033 172 fact that it was one of the clones that previously proved to be causing the level activity level. Mutagenesis was performed by extension PCR. The mutations and corresponding primers are listed in Table 5 and in FIG. 6. To create each mutant, two fragments were amplified. The left fragment was amplified by primers P1 (ATAGGCGCCAGCAACCGCAC) (SEQ ID NO: 21) and the reverse primer shown in Table 5. The right fragment was amplified by the forward primer presented in Table 6 and P2 primer (GCAGCAGCCAACTCAGCTTC) (SEQ ID NO: 22). Each PCR amplification reaction contained 30 pmol of each primer and 100 ng of template DNA. Amplifications were performed with Pfu Ultra II Hotstart DNA polymerase (Agilent cat # 600850-51). The reaction mixture of pCR (20 μL) was initially heated at 95 ° C for 2.5 min followed by 30 denaturation cycles at 94 ° C for 15 sec, annealing at 55 ° C for 15 sec. and elongation at 72 ° C for 1 min. After amplification, the PCR fragment was gel purified by the QIAGENO gel band purification kit and mixed (50 ng of each fragment). These mixtures served as a template for extension PCR by GibsV4ins-for (TTGTTTAACTTTAAGAAGGAGATTAC) and GibsV3ins-rev (GGCTTTGTTAGCAGCCGGATCT) primers (SEQ ID NO: 23-24, respectively) to generate a full-length gene fragment. The PCR conditions were the same as those described above. The full length DNA fragment was gel purified by the QIAGENO gel band purification kit. Then, 4 μl (about 0.3 pmol) of the PCR fragment was mixed with 1 μl of the amplified cloning vector (about 0.05 pmoles) and 5 μl of 2x Gibson Assembly mixture (New England Biolabs, cat # M5510AA) and incubated for 1 h at 50 ° C. After incubation, each mixture was diluted with sterile water (4 times) and transformed into XL1Blue competent cells (Agilent) according to the manufacturer's protocol. The transformed cells were plated on LB plates containing 50 μg / ml kanamycin and incubated overnight at 37 ° C. The next morning, the colonies were removed by scraping the plate. Plasmid DNA was isolated with a Qiagen Miniprep kit and transformed into BL21 competent cells (DE3) (Invitrogen). The transformations were plated on LB plates containing 25 μg / ml kanamycin and incubated overnight at 37 ° C. The colonies obtained were taken in 400 μl of LB 101 medium containing 50 μg / ml of kanamycin in deep 96-well plates and still used in the screening of 1 ml of butadiene (see above). Clones that produced butadiene at levels comparable to or greater than those of the wild-type enzyme were cultured again in several replicates and retested using the same assay with 1 ml of butadiene (secondary screening). Variant Reverse primer reverse primer sequence clone 91 V1231 Removing 123V-R ACATTTCATTTTTGAGACTGCAATATCTAAGTCGTGG clone V2041 Removing 204V 91-R AGAGTTGCATTGTACAAAATAGTTGTCTGGTTCACAAAC clone M274F Removing 274M 91-R ATCCATTCCATGAATCATAGCTAACGTCCAAGCGGTTGT clone V275I Removing 91 275I-R GATCCATTCCATGCACGAAAGCTAACGTCCAAGCGGTTGT M274F, V275I 274F-275I-R ATCCATTCCATGAATGAAAGCTAACGTCCAAGCGGTTGT M274F M274F-R ATCCATTCCATGCACGAAAGCTAACGTCCAAGCGGTTGTA V275I V2751-R GATCCATTCCATGAATCATAGCTAACGTCCAAGCGGTTGT A324L A324L-R TAATAAAAGTGTGAATAAAGAGGCTAAACCCACACCACC R360Y R360Y-R GCCTGGGTGTTCGTAnGTAnGAGGCTAGCAGAAACGATGCTT F382W F382W-R-R V123I GTAACAGAGCACCCCATCCGGCATGTACTTTGGCAAG V1231 V2041 ACATTTCATTTTTGAAATTGCAATATCTAAGTCGTGG V204I CAGAGTTGCATTGAATAAAATAGTTGTCTGGTTCACAAAC-R [0379] Table 5. Sequences inverse primers (SEQ ID No. 25-36, respectively, in order of appearance) used to create mutations to deconvolute the clone 91 Sequencing Variant Sequencing the sense primer Removing V1231 of 123V-F TTAGATATTGCAGTCTCAAAAATGAAATGTAAACGTGTATG 102 clone 91 V2041 Removing the clone 91-F 204V GACAACTATTTTGTACAATGCAACTCTGTGGCCTATTT clone M274F Removing 274M 91-F TGGACGTTAGCTATGATTCATGGAATGGATCCTGCCTTTTC clone V275I Removing 91 275I-F TGGACGTTAGCTTTCGTGCATGGAATGGATCCTGCCTTTTC M274F, V275I 274F -275I-F TGGACGTTAGCTTTCATTCATGGAATGGATCCTGCCTTTTC M274F M274F-F GCTTGGACGTTAGCTTTCGTGCATGGAATGGATCCTGCCTT V275I V2751-F ACGTTAGCTATGATTCATGGAATGGATCCTGCCTTTTC A324L A324L-F GTGGGTTTAGCCTCTTTATTCACACTTTTATTAGCCCGCGAAA R360Y R360Y-F GTTTCTGCTAGCCTCTACTACGAACACCCAGGCAGCCT F382W F382W-F CAAAGTACATGCCGGATGGGGTGCTCTGTTACGTATGC V1231 V1 23I-F TTAGATATTGCAATTTCAAAAATGAAATGTAAACGTGTATG V2041 V204I GACAACTATTTTATTCAATGCAACTCTGTGGCCTATTT-F [0380] Table 6. Sequences of the primers sense (SEQ ID No. 37-48, respectively, in order of appearance) used to create mutations to deconvolate clone 9. [0381] A summary of the screening results is presented in Table 7.
[0010] Several variants exhibited increased production of butadiene. They had the following combination of mutations: V123I / V2041 / M274F; M274F / V275I / F382W; V275I / A324L; V275I; V1231; and V2041. Mutant Variant Relative Production of Butadiene (WT = 1) Standard Deviation V2041, M274F, V2751 1.08 0.03 103 3033 172 2 V1 23I, M274F, V2751 0.74 3 V1231, V2041, V275I 0.89 0.17 4 V1 23I, V2041, M274F 1.265 0.01 M274F, V2751 0.45 0.16 M274F, A324L 0.55 M274F, R360Y 0.67 M274F, V2751, A324L 0.815 0.3 11 M274F, V275I, F382W 1.705 0.64 13 M274F, A324L, F382W 0.725 0.5 17 M274F, V275I, R360Y, F382W 0.905 0.42 21 V2751, A324L 1.66 0.34 23 V2751, F382W 0.84 0.07 24 V2751, A324L, R360Y 0.65 0.06 V2751, A324L, F382W 0.635 0.25 31 R360Y, F382W 1.235 0.47 32 M274F 0.675 0.01 33 V275I 2.135 0.33 34 A324L 1.64 0.04 R360Y 1,925 0.02 36 F382W 0.72 0.1 37 V1231 1.925 0.6 38 V2041 1.55 0.07 WT WT cdLD 1 0 clone 91 clone 91 1.425 0.15 Table 7. Relative production of butadiene by periplasmic variants of cdLD. [0384] b. Combinatoric Mutagenesis [0385] Many mutants have been created by combining two or more of the enhancement mutations defined in the preceding paragraphs. More specifically, several mutations have been imposed in addition to the following background mutants: A324L, S366V, A324L-S366G, M274-F96L and F382WL328V. Clones which produced butadiene at levels comparable to or greater than those of the wild type enzyme were cultured again in several replicates and re-tested using the same 1 ml test of butadiene (secondary screening). ). The results of testing of these clones are shown on FIG. 13. The addition of most of the mutations tested to A324L or S366V was not found to improve cdLD activity. Many of the variants did not have butadiene production. Therefore, it has been assumed that these mutations have low combinatorial potential. The mutation association (A324L and S366V) generated a variant without activity. At the same time, the addition of mutations to the combination A324L and S366G generated several combinations showing signs of increase (addition of H84A and V1231). Addition of R170D F96L and F382W mutations to the combination of M274-F96L and the I187M mutation to the combination of F382W-L328V also appeared to enhance production of butadiene production in the 1 mL test. These variants were retested in the secondary screen (FIGURE 14) and only two variants showed superior butadiene production relative to wild-type cdLDs: the combination of A324L, S366G and F382W, L328V, I187M. [0387] Some of these mutants were purified as described in Example 2 and tested again to determine if their specific activity was greater than that of cdLD. The purified proteins were diluted to the same concentration. 250 μl of purified protein solution was transferred to a crimp vial with 2.5 μl of 1.1 M 3-buten-2-ol (11 mM final concentration), sealed and incubated at room temperature for 72 h. After incubation, the samples were analyzed by a Shimadzu GCMS-QP2010 Ultra with Agilent HP PLOT / Q column (0.32 mm, 15 m in length, 20 μm in diameter) as previously for the 1 ml assay. butadiene. The results are presented in FIGURE 15. The two variants (combination of A324L, S366G and F382W, L328V, I187M) produce more butadiene than wild-type cdLD, with up to 3x the amount of butadiene produced for the A324L variant. , S366G. [0388] 10. Sequences of the polypeptides described herein. Description abbreviated.

权利要求:
Claims (4)
[0001]
1. A polypeptide comprising an amino acid sequence having an amino acid sequence homology of at least 90% with SEQ ID NO: 1, wherein said amino acid sequence comprises one to five X-position mutations SEQ ID NO: 1: R1_95X96R97-98X99R100-122X123R124-186X187R188-203X204 8205-211X212R213-272X273X274X275 8276-323X3248325-327X3288329-R359X3608361-365X3668367-381X3828383-398, wherein: X382 is mutated to a different amino acid selected from W and equivalent amino acids, optionally F382W: X328 is mutated to a different amino acid selected from V and equivalent amino acids, optionally L328V; X187 is mutated to a different amino acid selected from M and equivalent amino acids, optionally I187M; X96 is mutated to a different amino acid selected from L and equivalent amino acids; X99 is mutated to a different amino acid selected from L and equivalent amino acids; X123 is mutated to a different amino acid selected from I and equivalent amino acids; X204 is mutated to a different amino acid selected from I and equivalent amino acids; X212 is mutated to a different amino acid selected from F, Y, and equivalent amino acids; 961X273 is mutated to a different amino acid selected from C and equivalent amino acids; X274 is mutated to a different amino acid selected from F and equivalent amino acids; X275 is mutated to a different amino acid selected from I and equivalent amino acids; X324 is mutated to a different amino acid selected from L, E, and equivalent amino acids; X360 is mutated to a different amino acid selected from Y and equivalent amino acids; X366 is mutated to a different amino acid selected from V, C, G, and equivalent amino acids; and each R is the same as the corresponding amino acid in SEQ ID NO: 1; and optionally wherein the amino acid sequence comprises at least one mutation selected from F382W, L328V and 1187M, preferably all three, more preferably including the amino acid sequence of SEQ ID NO: 462 or SEQ. ID NO: 462 without the periplasmic label.
[0002]
The polypeptide of claim 1, wherein X187 is mutated to a different amino acid selected from M and equivalent amino acids.
[0003]
The polypeptide of claim 1, wherein X328 is mutated to a different amino acid selected from V and equivalent amino acids.
[0004]
The polypeptide of claim 1, wherein X382 is mutated to a different amino acid selected from W and equivalent amino acids. 962. The polypeptide of claim 1 comprising the following two mutations: F382W and L328V; preferably, comprising only these two mutations. The polypeptide of claim 1 comprising the following three mutations: F382W, L328V and 1187M; preferably, comprising only these three mutations. A polypeptide comprising a sequence selected from the sequence listing of Annex 3 (SEQ ID NO: 124-458). 8. A polypeptide comprising a sequence selected from the sequence list of Table 9 (SEQ ID NO: 4 and SEQ ID NO: 88-123). The polypeptide of any one of claims 1 to 8, wherein said amino acid sequence further comprises a C-terminal His tag (His6 or SEQ ID NO: 6). The polypeptide according to any one of claims 1 to 9, wherein said amino acid sequence is devoid of periplasmic tag (SEQ ID NO: 3). Polypeptide according to any one of claims 1 to 9, the polypeptide having an activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene which is at least 80% of that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, increased by a factor of about 1.5 or greater relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably by a factor of about 2 or more relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor of 2.5 or higher than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor of 3 or greater than that of a polypeptide consisting of SEQ ID NO: 1 , 4, 5, 7, or 8, preferably about 3.5 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably a factor of about 4 or more per ort to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 4.5 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1 , 4, 5, 7 or 8 or preferably a factor of about 5 or more with respect to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, and wherein said activity is observed in at least one activity test. The polypeptide of claim 11, wherein said activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene is observed in at least one type of non-bacterial cell. The polypeptide of claim 11, wherein said activity in catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene is observed in at least one type of bacteria. The polypeptide according to any one of claims 1 to 13, the polypeptide having an activity in catalyzing the dehydration of 3-buten-2-ol to isoprene which is at least 80% of that of a polypeptide consisting of of SEQ ID NO: 1, 4, 5, 7 or 8, increased by a factor of about 1.5 or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably by a factor of about 2 or more with respect to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about a factor of 2.5 or greater with respect to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably a factor of about 3 or greater relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5 , 7, or 8, preferably 964, about 3.5 fold or greater than a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 4 fold. or higher compared to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 4.5 fold or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8 or preferably by a factor of about 5 or more with respect to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, or preferably a factor of 15 about or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8 wherein said activity is observed in at least one activity assay or preferably about 55 fold. or greater than that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, preferably about 30 fold or greater than that of a polypeptide consisting of SEQ ID NO 1, 4, 5, 7 or 8, and wherein said activity is observed in at least one activity assay. The polypeptide of claim 14 wherein said activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene is observed in at least one type of non-bacterial cell. The polypeptide of claim 14 wherein said activity in catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene is observed in at least one type of bacteria. A polynucleotide comprising, consisting of or consisting essentially of a nucleic acid encoding any of the polypeptides according to any one of claims 1 to 16, preferably with codon optimization. The polynucleotide of claim 17, wherein the polynucleotide is either a DNA molecule or an RNA molecule. The DNA molecule of claim 18, further comprising a promoter operably linked to the nucleic acid sequence encoding the polypeptide or derivative. A recombinant expression vector comprising a DNA molecule according to any one of claims 17 to 19. 21. A host cell which is transformed or transduced with a DNA molecule according to any one of claims 17 to 19 or with a recombinant expression vector according to claim 20. The cell of claim 21, wherein the DNA molecule or the recombinant expression vector are integrated into a chromosome of the cell. 23. A non-human organism, preferably a microorganism, comprising a heterologous DNA molecule encoding a polypeptide according to any one of claims 1 to 16. 24. Non-human animal or transgenic plant comprising a heterologous DNA molecule encoding a polypeptide according to any one of claims 1 to 16. 25. The microorganism of claim 23 wherein the microorganism is a bacterium or a fungus. A process for producing a polypeptide according to any one of claims 1 to 16, the method comprising: (i) preparing an expression construct which comprises a polynucleotide according to claim 17, with a coding sequence for the polypeptide according to any one of claims 1 to 16 operably linked to one or more regulatory nucleotide sequences; (ii) transfection or transformation of an appropriate host cell with the expression construct; (iii) expressing the recombinant polypeptide in said host cell; and (iv) isolating or purifying the recombinant polypeptide from said host cell or using the host cell obtained as such or as a cell extract. 27. A process for producing a polypeptide having an activity of at least 80% or improved activity, in (i) catalyzing the dehydration of 3-buten-2-ol to 1,3-butadiene and / or ii) catalyzing the dehydration of 3-methyl-3-buten-2-ol to isoprene, relative to that of a polypeptide consisting of SEQ ID NO: 1, 4, 5, 7 or 8, the process comprising Preparation of a polypeptide according to any one of Claims 1 to 16. 28. Composition comprising one or more polypeptides according to any one of Claims 1 to 16. 29. Composition according to Claim 28, further comprising the polypeptide of SEQ ID NO: 1, with or without an N-terminal periplasmic tag and with or without the first Met. 30. Composition according to any one of claims 28 to 29, further comprising 3-buten-2-ol and / or 3-methyl-3-buten-2-ol. 31. A composition according to any one of claims 28 to 30, further comprising 1,3-butadiene and / or isoprene. A composition comprising (i) a rubber product polymerized from 1,3-butadiene produced in the presence of a polypeptide according to any one of claims 1 to 16 and / or (ii) a product based on 967 3033 1 72 rubber polymerized from isoprene produced in the presence of a polypeptide according to any one of claims 14 to 16. 33. Composition comprising a copolymer polymerized from 1,3-butadiene produced in the presence of a polypeptide according to any one of claims 1 to 16; and / or a rubber product polymerized from 1,3-butadiene produced in the presence of a polypeptide according to any one of claims 14 to 16. 34. Composition comprising a polymer-based plastic product from 1,3-butadiene produced in the presence of a polypeptide according to any one of claims 1 to 16; and / or a polymerized plastic product from isoprene produced in the presence of a polypeptide according to any one of claims 14 to 16. 35. An antibody capable of binding to a polypeptide according to any of claims 1 16. A fusion protein comprising a polypeptide according to any one of claims 1 to 16. 37. A complex comprising a polypeptide according to any one of claims 1 to 16, said complex optionally further comprising 3-methyl 3-buten-2-ol. 38. Complex comprising a polypeptide according to any one of claims 1 to 16, said complex further comprising optionally 3-buten-2-ol. 39. Crystal having the coordinates defined in Appendix I in space group P2 (1) with cellular parameters a = 133.18A, b = 110.83A, c = 162.20A, which is produced from of a polypeptide consisting of the amino acid sequence of SEQ ID NO: 5 with up to 2% variation in any cell size. 40. Crystal comprising the coordinates defined in Annex 2 in space group P2 (1) with cellular parameters a = 88.7 A, b = 111.22 A, c = 120.42 A, which is produced from of a polypeptide consisting of the amino acid sequence of SEQ ID NO: 9 with up to 2% of variation in any cell size. 41. A process for producing isoprene, myrcene, and / or 1,3-butadiene, comprising the cultivation or growth of a host cell or organism according to any of claims 21 to 25 in conditions and for a time sufficient to produce isoprene, myrcene and / or 1,3-butadiene. 42. A culture medium comprising isoprene, myrcene, and / or 1,3-butadiene, wherein said isoprene, myrcene, and / or 1,3-butadiene, is a carbon-carbon isotope ratio. -13 and carbon-14 which reflects an absorption source of atmospheric carbon dioxide. 43. A culture medium according to claim 42, said culture medium being separated from a host cell or organism according to any one of claims 21 to 25. Isoprene, myrcene and / or 1,3-butadiene bioreactor having an isotopic ratio of carbon-12, carbon-13 and carbon-14 which reflects an absorption source of atmospheric carbon dioxide, preferably produced by culturing a host cell or organism according to any one of Claims 21 to 25. 969. Isoprene, myrcene and / or 1,3-butadiene, bioderivated according to claim 44, said isoprene, myrcene and / or 1,3-butadiene, having a Fm value of at least 80 ° / ( :), at least 85 ° / (:), at least 90 ° / (:), at least 95% or at least 98%. 46. A composition comprising isoprene, myrcene, and / or 1,3-butadiene bioremedic according to any one of claims 44 to 45 and a compound other than said isoprene, myrcene and / or 1,3-butadiene bioderivated. 47. The composition according to claim 46, wherein said compound other than said isoprene, myrcene and / or 1,3-butadiene is a trace amount of a cell part of a host cell or an organism according to one of Any one of claims 21 to 25. 48. A bioderivative polymer comprising isoprene, myrcene, and / or 1,3-butadiene, as claimed in any one of claims 44 to 45. 49. A bio-based resin comprising isoprene , Myrcene, and / or 1,3-butadiene, as claimed in any one of Claims 44 to 45. 50. A molded product obtained by molding a bioderected polymer according to Claim 48. 51. A method for producing a A bioderivative polymer as claimed in claim 48 comprising the chemical reaction of isoprene, myrcene, and / or 1,3-butadiene, as claimed in claim 44 or 46, with itself or with another compound in a polymer-producing reaction. 52. A molded product obtained by molding a bioderivative resin according to claim 49. 53. A process for producing a bioderivative resin according to claim 49 comprising the chemical reaction of said isoprene, myrcene, and / or 970,3-butadiene with itself or another compound in a resin production reaction. 971

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引用文献:

---

公开号 | 申请日 | 公开日 | 申请人 | 专利标题

---

WO2014184345A1|2013-05-17|2014-11-20|Global Bioenergies|Alkenol dehydratase variants|

---

WO2016075244A1|2014-11-13|2016-05-19|Global Bioenergies|Alkenol dehydratase variants|

---

US4554101A|1981-01-09|1985-11-19|New York Blood Center, Inc.|Identification and preparation of epitopes on antigens and allergens on the basis of hydrophilicity|

---

US8340951B2|2007-12-13|2012-12-25|University Of Washington|Synthetic enzymes derived from computational design|

---

JP6058650B2|2011-06-17|2017-01-11|インビスタ テクノロジーズ エス．アー．エール．エル．|Use of hydrolases to increase monomer content in waste streams|

---

CN104769119A|2012-06-15|2015-07-08|英威达技术有限责任公司|Methods for biosynthesizing 1,3 butadiene|

---

US8703455B2|2012-08-29|2014-04-22|Scientist of Fourtune, S.A.|Production of volatile dienes by enzymatic dehydration of light alkenols|

---

EP2935364A2|2012-12-21|2015-10-28|Danisco US Inc.|Production of isoprene, isoprenoid, and isoprenoid precursors using an alternative lower mevalonate pathway|

---

WO2015000981A2|2013-07-03|2015-01-08|Scientist Of Fortune S.A.|Method for the enzymatic production of 3-buten-2-one|

---

CN105683385A|2013-08-05|2016-06-15|英威达技术有限责任公司|Methods for biosynthesis of isoprene|

---

US9220742B1|2015-02-27|2015-12-29|Invista North America S.A.R.L.|Mutant polypeptides and uses thereof|CN107849101A|2015-02-27|2018-03-27|英威达技术有限责任公司|New polypeptide and application thereof|

---

US9220742B1|2015-02-27|2015-12-29|Invista North America S.A.R.L.|Mutant polypeptides and uses thereof|

---

CN108026214B|2015-05-30|2021-03-02|基因组股份公司|Vinyl isomerase-dehydratase, enol-dehydratase, linalool-dehydratase and/or crotyl alcohol dehydratase, and preparation and use thereof|

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US201562126279P| true| 2015-02-27|2015-02-27|

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