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Mareya TM, Coady TM, O'Reilly C, Kinsella M, Coffey L, Lennon CM. Process Optimisation Studies and Aminonitrile Substrate Evaluation of Rhodococcus erythropolis SET1, A Nitrile Hydrolyzing Bacterium. ChemistryOpen 2020; 9:512-520. [PMID: 32346499 PMCID: PMC7184877 DOI: 10.1002/open.202000088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Indexed: 11/16/2022] Open
Abstract
A comprehensive series of optimization studies including pH, solvent and temperature were completed on the nitrile hydrolyzing Rhodococcus erythropolis bacterium SET1 with the substrate 3-hydroxybutyronitrile. These identified temperature of 25 °C and pH of 7 as the best conditions to retain enantioselectivity and activity. The effect of the addition of organic solvents to the biotransformation mixture was also determined. The results of the study suggested that SET1 is suitable for use in selected organo-aqueous media at specific ratios only. The functional group tolerance of the isolate with unprotected and protected β-aminonitriles, structural analogues of β-hydroxynitriles was also investigated with disappointingly poor isolated yields and selectivity obtained. The isolate was further evaluated with the α- aminonitrile phenylglycinonitrile generating acid in excellent yield and ee (>99 % (S) - isomer and 50 % yield). A series of pH studies with this substrate indicated pH 7 to be the optimum pH to avoid product and substrate degradation.
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Affiliation(s)
- Tatenda M. Mareya
- Department of ScienceWaterford Institute of TechnologyCork RoadWaterfordX91K0EKIreland
| | - Tracey M. Coady
- Department of ScienceWaterford Institute of TechnologyCork RoadWaterfordX91K0EKIreland
| | - Catherine O'Reilly
- Department of ScienceWaterford Institute of TechnologyCork RoadWaterfordX91K0EKIreland
| | - Michael Kinsella
- Department of ScienceWaterford Institute of TechnologyCork RoadWaterfordX91K0EKIreland
| | - Lee Coffey
- Department of ScienceWaterford Institute of TechnologyCork RoadWaterfordX91K0EKIreland
| | - Claire M. Lennon
- Department of ScienceWaterford Institute of TechnologyCork RoadWaterfordX91K0EKIreland
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Villar-Acevedo G, Lugo-Mas P, Blakely MN, Rees JA, Ganas AS, Hanada EM, Kaminsky W, Kovacs JA. Metal-Assisted Oxo Atom Addition to an Fe(III) Thiolate. J Am Chem Soc 2016; 139:119-129. [PMID: 28033001 DOI: 10.1021/jacs.6b03512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cysteinate oxygenation is intimately tied to the function of both cysteine dioxygenases (CDOs) and nitrile hydratases (NHases), and yet the mechanisms by which sulfurs are oxidized by these enzymes are unknown, in part because intermediates have yet to be observed. Herein, we report a five-coordinate bis-thiolate ligated Fe(III) complex, [FeIII(S2Me2N3(Pr,Pr))]+ (2), that reacts with oxo atom donors (PhIO, IBX-ester, and H2O2) to afford a rare example of a singly oxygenated sulfenate, [FeIII(η2-SMe2O)(SMe2)N3(Pr,Pr)]+ (5), resembling both a proposed intermediate in the CDO catalytic cycle and the essential NHase Fe-S(O)Cys114 proposed to be intimately involved in nitrile hydrolysis. Comparison of the reactivity of 2 with that of a more electron-rich, crystallographically characterized derivative, [FeIIIS2Me2NMeN2amide(Pr,Pr)]- (8), shows that oxo atom donor reactivity correlates with the metal ion's ability to bind exogenous ligands. Density functional theory calculations suggest that the mechanism of S-oxygenation does not proceed via direct attack at the thiolate sulfurs; the average spin-density on the thiolate sulfurs is approximately the same for 2 and 8, and Mulliken charges on the sulfurs of 8 are roughly twice those of 2, implying that 8 should be more susceptible to sulfur oxidation. Carboxamide-ligated 8 is shown to be unreactive towards oxo atom donors, in contrast to imine-ligated 2. Azide (N3-) is shown to inhibit sulfur oxidation with 2, and a green intermediate is observed, which then slowly converts to sulfenate-ligated 5. This suggests that the mechanism of sulfur oxidation involves initial coordination of the oxo atom donor to the metal ion. Whether the green intermediate is an oxo atom donor adduct, Fe-O═I-Ph, or an Fe(V)═O remains to be determined.
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Affiliation(s)
- Gloria Villar-Acevedo
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Priscilla Lugo-Mas
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Maike N Blakely
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julian A Rees
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Abbie S Ganas
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Erin M Hanada
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Werner Kaminsky
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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Duca D, Lorv J, Patten CL, Rose D, Glick BR. Indole-3-acetic acid in plant-microbe interactions. Antonie van Leeuwenhoek 2014; 106:85-125. [PMID: 24445491 DOI: 10.1007/s10482-013-0095-y] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/07/2013] [Indexed: 01/04/2023]
Abstract
Indole-3-acetic acid (IAA) is an important phytohormone with the capacity to control plant development in both beneficial and deleterious ways. The ability to synthesize IAA is an attribute that many bacteria including both plant growth-promoters and phytopathogens possess. There are three main pathways through which IAA is synthesized; the indole-3-pyruvic acid, indole-3-acetamide and indole-3-acetonitrile pathways. This chapter reviews the factors that effect the production of this phytohormone, the role of IAA in bacterial physiology and in plant-microbe interactions including phytostimulation and phytopathogenesis.
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Affiliation(s)
- Daiana Duca
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada,
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Araújo R, Casal M, Cavaco-Paulo A. Application of enzymes for textile fibres processing. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420802390457] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Enhanced production of amidase from Rhodococcus erythropolis MTCC 1526 by medium optimisation using a statistical experimental design. J Ind Microbiol Biotechnol 2009; 36:671-8. [DOI: 10.1007/s10295-009-0536-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
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6
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Lugo-Mas P, Taylor W, Schweitzer D, Theisen RM, Xu L, Shearer J, Swartz RD, Gleaves MC, Dipasquale A, Kaminsky W, Kovacs JA. Properties of square-pyramidal alkyl-thiolate Fe(III) complexes, including an analogue of the unmodified form of nitrile hydratase. Inorg Chem 2008; 47:11228-36. [PMID: 18989922 PMCID: PMC2659597 DOI: 10.1021/ic801704n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The syntheses and structures of three new coordinatively unsaturated, monomeric, square-pyramidal thiolate-ligated Fe(III) complexes are described, [Fe(III)((tame-N(3))S(2)(Me2))](+) (1), [Fe(III)(Et-N(2)S(2)(Me2))(py)](1-) (3), and [Fe(III)((tame-N(2)S)S(2)(Me2))](2-) (15). The anionic bis-carboxamide, tris-thiolate N(2)S(3) coordination sphere of 15 is potentially similar to that of the yet-to-be characterized unmodified form of NHase. Comparison of the magnetic and reactivity properties of these reveals how anionic charge build up (from cationic 1 to anionic 3 and dianionic 15) and spin-state influence apical ligand affinity. For all of the ligand-field combinations examined, an intermediate S = 3/2 spin state was shown to be favored by a strong N(2)S(2) basal plane ligand field, and this was found to reduce the affinity for apical ligands, even when they are built in. This is in contrast to the post-translationally modified NHase active site, which is low spin and displays a higher affinity for apical ligands. Cationic 1 and its reduced Fe(II) precursor are shown to bind NO and CO, respectively, to afford [Fe(III)((tame-N(3))S(2)(Me))(NO)](+) (18, nu(NuO) = 1865 cm(-1)), an analogue of NO-inactivated NHase, and [Fe(II)((tame-N(3))S(2)(Me))(CO)] (16; nu(CO) stretch (1895 cm(-1)). Anions (N(3)(-), CN(-)) are shown to be unreactive toward 1, 3, and 15 and neutral ligands unreactive toward 3 and 15, even when present in 100-fold excess and at low temperatures. The curtailed reactivity of 15, an analogue of the unmodified form of NHase, and its apical-oxygenated S = 3/2 derivative [Fe(III)((tame-N(2)SO(2))S(2)(Me2))](2-) (20) suggests that regioselective post-translational oxygenation of the basal plane NHase cysteinate sulfurs plays an important role in promoting substrate binding. This is supported by previously reported theoretical (DFT) calculations.
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Affiliation(s)
- Priscilla Lugo-Mas
- The Department of Chemistry, University of Washington, Box 351700 Seattle, Washington 98195-1700, USA
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Ewert C, Lutz-Wahl S, Fischer L. Enantioselective conversion of α-arylnitriles by Klebsiella oxytoca. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Yeom SJ, Kim HJ, Oh DK. Enantioselective production of 2,2-dimethylcyclopropane carboxylic acid from 2,2-dimethylcyclopropane carbonitrile using the nitrile hydratase and amidase of Rhodococcus erythropolis ATCC 25544. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Conversion of mandelonitrile and phenylglycinenitrile by recombinant E. coli cells synthesizing a nitrilase from Pseudomonas fluorescens EBC191. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.05.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vink MKS, Wijtmans R, Reisinger C, van den Berg RJF, Schortinghuis CA, Schwab H, Schoemaker HE, Rutjes FPJT. Nitrile hydrolysis activity ofRhodococcus erythropolis NCIMB 11540 whole cells. Biotechnol J 2006; 1:569-73. [PMID: 16892293 DOI: 10.1002/biot.200600028] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nitrile hydrolyzing properties of the bacterium strain Rhodococcus erythropolis NCIMB 11540 have been investigated. Using whole cells of the microorganism, a wide variety of aromatic and aliphatic cyanide-containing substrates was successfully hydrolyzed to the corresponding amide or acid. In the case of dicyanides, selective monohydrolysis took place, which was further explored in the desymmetrization of malononitriles resulting in the corresponding cyano amides in enantiomeric excesses of up to 98%.
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Affiliation(s)
- Mandy K S Vink
- J.H. van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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11
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de Carvalho CCCR, da Fonseca MMR. The remarkable Rhodococcus erythropolis. Appl Microbiol Biotechnol 2005; 67:715-26. [PMID: 15711940 DOI: 10.1007/s00253-005-1932-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 01/26/2005] [Accepted: 01/27/2005] [Indexed: 10/25/2022]
Abstract
Rhodococcus erythropolis cells contain a large set of enzymes that allow them to carry out an enormous number of bioconversions and degradations. Oxidations, dehydrogenations, epoxidations, hydrolysis, hydroxylations, dehalogenations and desulfurisations have been reported to be performed by R. erythropolis cells or enzymes. This large array of enzymes fully justifies the prospective application of this bacterium in biotechnology.
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Affiliation(s)
- Carla C C R de Carvalho
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais, Lisboa, 1049-001, Portugal.
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Chilov GG, Moody HM, Boesten WH, Švedas VK. Resolution of (RS)-phenylglycinonitrile by penicillin acylase-catalyzed acylation in aqueous medium. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0957-4166(03)00523-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Hensel M, Lutz-Wahl S, Fischer L. Stereoselective hydration of (RS)-phenylglycine nitrile by new whole cell biocatalysts. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0957-4166(02)00751-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Trott S, Bürger S, Calaminus C, Stolz A. Cloning and heterologous expression of an enantioselective amidase from Rhodococcus erythropolis strain MP50. Appl Environ Microbiol 2002; 68:3279-86. [PMID: 12089004 PMCID: PMC126760 DOI: 10.1128/aem.68.7.3279-3286.2002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene for an enantioselective amidase was cloned from Rhodococcus erythropolis MP50, which utilizes various aromatic nitriles via a nitrile hydratase/amidase system as nitrogen sources. The gene encoded a protein of 525 amino acids which corresponded to a protein with a molecular mass of 55.5 kDa. The deduced complete amino acid sequence showed homology to other enantioselective amidases from different bacterial genera. The nucleotide sequence approximately 2.5 kb upstream and downstream of the amidase gene was determined, but no indications for a structural coupling of the amidase gene with the genes for a nitrile hydratase were found. The amidase gene was carried by an approximately 40-kb circular plasmid in R. erythropolis MP50. The amidase was heterologously expressed in Escherichia coli and shown to hydrolyze 2-phenylpropionamide, alpha-chlorophenylacetamide, and alpha-methoxyphenylacetamide with high enantioselectivity; mandeloamide and 2-methyl-3-phenylpropionamide were also converted, but only with reduced enantioselectivity. The recombinant E. coli strain which synthesized the amidase gene was shown to grow with organic amides as nitrogen sources. A comparison of the amidase activities observed with whole cells or cell extracts of the recombinant E. coli strain suggested that the transport of the amides into the cells becomes the rate-limiting step for amide hydrolysis in recombinant E. coli strains.
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Affiliation(s)
- Sandra Trott
- Institut für Mikrobiologie, Universität Stuttgart, 70569 Stuttgart, Germany
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15
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16
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Noveron JC, Olmstead MM, Mascharak PK. A synthetic analogue of the active site of Fe-containing nitrile hydratase with carboxamido N and thiolato S as donors: synthesis, structure, and reactivities. J Am Chem Soc 2001; 123:3247-59. [PMID: 11457060 DOI: 10.1021/ja001253v] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of our work on models of the iron(III) site of Fe-containing nitrile hydratase, a designed ligand PyPSH(4) with two carboxamide and two thiolate donor groups has been synthesized. Reaction of (Et(4)N)[FeCl(4)] with the deprotonated form of the ligand in DMF affords the mononuclear iron(III) complex (Et(4)N)[Fe(III)(PyPS)] (1) in high yield. The iron(III) center is in a trigonal bipyramidal geometry with two deprotonated carboxamido nitrogens, one pyridine nitrogen, and two thiolato sulfurs as donors. Complex 1 is stable in water and binds a variety of Lewis bases at the sixth site at low temperature to afford green solutions with a band around 700 nm. The iron(III) centers in these six-coordinate species are low-spin and exhibit EPR spectra much like the enzyme. The pK(a) of the water molecule in [Fe(III)(PyPS)(H(2)O)](-) is 6.3 +/- 0.4. The iron(III) site in 1 with ligated carboxamido nitrogens and thiolato sulfurs does not show any affinity toward nitriles. It thus appears that at physiological pH, a metal-bound hydroxide promotes hydration of nitriles nested in close proximity of the iron center in the enzyme. Redox measurements demonstrate that the carboxamido nitrogens prefer Fe(III) to Fe(II) centers. This fact explains the absence of any redox behavior at the iron site in nitrile hydratase. Upon exposure to limited amount of dioxygen, 1 is converted to the bis-sulfinic species. The structure of the more stable O-bonded sulfinato complex (Et(4)N)[Fe(III)(PyP[SO(2)](2))] (2) has been determined. Six-coordinated low-spin cyanide adducts of the S-bonded and the O-bonded sulfinato complexes, namely, Na(2)[Fe(III)(PyP[SO(2)](2))(CN)] (4) and (Et(4)N)(2)[Fe(III)(PyP[SO(2)](2))(CN)] (5), afford green solutions in water and other solvents. The iron(II) complex (Et(4)N)(2)[Fe(II)(PyPS)] (3) has also been isolated and structurally characterized.
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Affiliation(s)
- J C Noveron
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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López-Serrano P, Jongejan J, van Rantwijk F, Sheldon R. Enantioselective acylation of α-aminonitriles catalysed by Candida antarctica lipase. An unexpected turnover-related racemisation. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0957-4166(01)00011-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Wegman MA, Heinemann U, Stolz A, van Rantwijk F, Sheldon RA. Stereoretentive Nitrile Hydratase-Catalysed Hydration of d-Phenylglycine Nitrile. Org Process Res Dev 2000. [DOI: 10.1021/op000055l] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. A. Wegman
- Laboratory of Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Institut für Mikrobiologie der Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - U. Heinemann
- Laboratory of Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Institut für Mikrobiologie der Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - A. Stolz
- Laboratory of Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Institut für Mikrobiologie der Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - F. van Rantwijk
- Laboratory of Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Institut für Mikrobiologie der Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - R. A. Sheldon
- Laboratory of Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Institut für Mikrobiologie der Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Abstract
A number of nitrile-related enzymes have been screened over the past year for use in synthetic applications. There have also been significant advances in our understanding of the structures and modes of regulation of metal-containing nitrile hydratases. Enzyme structural characterization has provided new insights into how the molecular structure determines the enzyme function and how an enzyme can be endowed with new properties. This information has important implications for potential future applications other than the present industrial production of acrylamide and nicotinamide.
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Affiliation(s)
- M Kobayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Institute of Applied Biochemistry, The University of Tsukuba, Kyoto, Tsukuba, 305-8572, Japan
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