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Feng C, Chen J, Ye W, Wang Z. Nitrile hydratase as a promising biocatalyst: recent advances and future prospects. Biotechnol Lett 2024:10.1007/s10529-024-03530-y. [PMID: 39269672 DOI: 10.1007/s10529-024-03530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/05/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
Amides are an important type of synthetic intermediate used in the chemical, agrochemical, pharmaceutical, and nutraceutical industries. The traditional chemical process of converting nitriles into the corresponding amides is feasible but is restricted because of the harsh conditions required. In recent decades, nitrile hydratase (NHase, EC 4.2.1.84) has attracted considerable attention because of its application in nitrile transformation as a prominent biocatalyst. In this review, we provide a comprehensive survey of recent advances in NHase research in terms of natural distribution, enzyme screening, and molecular modification on the basis of its characteristics and catalytic mechanism. Additionally, industrial applications and recent significant biotechnology advances in NHase bioengineering and immobilization techniques are systematically summarized. Moreover, the current challenges and future perspectives for its further development in industrial applications for green chemistry were also discussed. This study contributes to the current state-of-the-art, providing important technical information for new NHase applications in manufacturing industries.
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Affiliation(s)
- Chao Feng
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jing Chen
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Wenxin Ye
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Zhanshi Wang
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China.
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2
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Mashweu AR, Chhiba-Govindjee VP, Bode ML, Brady D. Substrate Profiling of the Cobalt Nitrile Hydratase from Rhodococcus rhodochrous ATCC BAA 870. Molecules 2020; 25:molecules25010238. [PMID: 31935987 PMCID: PMC6983157 DOI: 10.3390/molecules25010238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/22/2019] [Accepted: 12/26/2019] [Indexed: 02/04/2023] Open
Abstract
The aromatic substrate profile of the cobalt nitrile hydratase from Rhodococcus rhodochrous ATCC BAA 870 was evaluated against a wide range of nitrile containing compounds (>60). To determine the substrate limits of this enzyme, compounds ranging in size from small (90 Da) to large (325 Da) were evaluated. Larger compounds included those with a bi-aryl axis, prepared by the Suzuki coupling reaction, Morita-Baylis-Hillman adducts, heteroatom-linked diarylpyridines prepared by Buchwald-Hartwig cross-coupling reactions and imidazo[1,2-a]pyridines prepared by the Groebke-Blackburn-Bienaymé multicomponent reaction. The enzyme active site was moderately accommodating, accepting almost all of the small aromatic nitriles, the diarylpyridines and most of the bi-aryl compounds and Morita-Baylis-Hillman products but not the Groebke-Blackburn-Bienaymé products. Nitrile conversion was influenced by steric hindrance around the cyano group, the presence of electron donating groups (e.g., methoxy) on the aromatic ring, and the overall size of the compound.
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Affiliation(s)
- Adelaide R. Mashweu
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
| | - Varsha P. Chhiba-Govindjee
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
- CSIR Chemical Production Cluster, PO Box 395, Pretoria 0001, South Africa
| | - Moira L. Bode
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
- Correspondence: (M.L.B.); (D.B.); Tel.: +27-117176745 (D.B.)
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa; (A.R.M.); (V.P.C.-G.)
- Correspondence: (M.L.B.); (D.B.); Tel.: +27-117176745 (D.B.)
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Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Sci 2015; 24:762-78. [PMID: 25627867 PMCID: PMC4420525 DOI: 10.1002/pro.2648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/10/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues.
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Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Nicholas A DeLateur
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Srinivas Somarowthu
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Caitlyn L Mills
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Walter R Novak
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Dagmar Ringe
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
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Pettinati I, Brem J, McDonough MA, Schofield CJ. Crystal structure of human persulfide dioxygenase: structural basis of ethylmalonic encephalopathy. Hum Mol Genet 2015; 24:2458-69. [PMID: 25596185 PMCID: PMC4383860 DOI: 10.1093/hmg/ddv007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/13/2015] [Indexed: 01/08/2023] Open
Abstract
The ethylmalonic encephalopathy protein 1 (ETHE1) catalyses the oxygen-dependent oxidation of glutathione persulfide (GSSH) to give persulfite and glutathione. Mutations to the hETHE1 gene compromise sulfide metabolism leading to the genetic disease ethylmalonic encephalopathy. hETHE1 is a mono-iron binding member of the metallo-β-lactamase (MBL) fold superfamily. We report crystallographic analysis of hETHE1 in complex with iron to 2.6 Å resolution. hETHE1 contains an αββα MBL-fold, which supports metal-binding by the side chains of an aspartate and two histidine residues; three water molecules complete octahedral coordination of the iron. The iron binding hETHE1 enzyme is related to the ‘classical’ di-zinc binding MBL hydrolases involved in antibiotic resistance, but has distinctive features. The histidine and aspartate residues involved in iron-binding in ETHE1, occupy similar positions to those observed across both the zinc 1 and zinc 2 binding sites in classical MBLs. The active site of hETHE1 is very similar to an ETHE1-like enzyme from Arabidopsis thaliana (60% sequence identity). A channel leading to the active site is sufficiently large to accommodate a GSSH substrate. Some of the observed hETHE1 clinical mutations cluster in the active site region. The structure will serve as a basis for detailed functional and mechanistic studies on ETHE1 and will be useful in the development of selective MBL inhibitors.
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Affiliation(s)
- Ilaria Pettinati
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Jürgen Brem
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
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Hopmann KH. Full Reaction Mechanism of Nitrile Hydratase: A Cyclic Intermediate and an Unexpected Disulfide Switch. Inorg Chem 2014; 53:2760-2. [DOI: 10.1021/ic500091k] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Kathrin H. Hopmann
- Centre for Theoretical and
Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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Wang S, Dai Y, Wang J, Shen Y, Zhai Y, Zheng H, Wang M. Molecular insights into substrate specificity of Rhodococcus ruber CGMCC3090 by gene cloning and homology modeling. Enzyme Microb Technol 2013; 52:111-7. [DOI: 10.1016/j.enzmictec.2012.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 11/29/2022]
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7
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Brodkin HR, Novak WRP, Milne AC, D'Aquino JA, Karabacak NM, Goldberg IG, Agar JN, Payne MS, Petsko GA, Ondrechen MJ, Ringe D. Evidence of the participation of remote residues in the catalytic activity of Co-type nitrile hydratase from Pseudomonas putida. Biochemistry 2011; 50:4923-35. [PMID: 21473592 DOI: 10.1021/bi101761e] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues (α-Asp164, β-Glu56, and β-His147) and one predicted third-shell residue (β-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues (α-Glu168) and the three residues not predicted (α-Arg170, α-Tyr171, and β-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.
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Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology and Institute for Complex Scientific Software, Northeastern University, Boston, Massachusetts 02115, USA
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Okamoto S, Van Petegem F, Patrauchan MA, Eltis LD. AnhE, a metallochaperone involved in the maturation of a cobalt-dependent nitrile hydratase. J Biol Chem 2010; 285:25126-33. [PMID: 20558748 DOI: 10.1074/jbc.m110.109223] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetonitrile hydratase (ANHase) of Rhodococcus jostii RHA1 is a cobalt-containing enzyme with no significant sequence identity with characterized nitrile hydratases. The ANHase structural genes anhA and anhB are separated by anhE, predicted to encode an 11.1-kDa polypeptide. An anhE deletion mutant did not grow on acetonitrile but grew on acetamide, the ANHase reaction product. Growth on acetonitrile was restored by providing anhE in trans. AnhA could be used to assemble ANHase in vitro, provided the growth medium was supplemented with 50 microM CoCl(2). Ten- to 100-fold less CoCl(2) sufficed when anhE was co-expressed with anhA. Moreover, AnhA contained more cobalt when produced in cells containing AnhE. Chromatographic analyses revealed that AnhE existed as a monomer-dimer equilibrium (100 mm phosphate, pH 7.0, 25 degrees C). Divalent metal ions including Co(2+), Cu(2+), Zn(2+), and Ni(2+) stabilized the dimer. Isothermal titration calorimetry studies demonstrated that AnhE binds two half-equivalents of Co(2+) with K(d) of 0.12 +/- 0.06 nM and 110 +/- 35 nM, respectively. By contrast, AnhE bound only one half-equivalent of Zn(2+) (K(d) = 11 +/- 2 nM) and Ni(2+) (K(d) = 49 +/- 17 nM) and did not detectably bind Cu(2+). Substitution of the sole histidine residue did not affect Co(2+) binding. Holo-AnhE had a weak absorption band at 490 nM (epsilon = 9.7 +/- 0.1 m(-1) cm(-1)), consistent with hexacoordinate cobalt. The data support a model in which AnhE acts as a dimeric metallochaperone to deliver cobalt to ANHase. This study provides insight into the maturation of NHases and metallochaperone function.
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Affiliation(s)
- Sachi Okamoto
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
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10
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Modeling catalytic mechanism of nitrile hydratase by semi-empirical quantum mechanical calculation. J Mol Graph Model 2008; 27:522-8. [DOI: 10.1016/j.jmgm.2008.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 08/26/2008] [Accepted: 09/02/2008] [Indexed: 11/20/2022]
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11
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Hopmann KH, Himo F. Theoretical Investigation of the Second-Shell Mechanism of Nitrile Hydratase. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200701137] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Song L, Wang M, Shi J, Xue Z, Wang MX, Qian S. High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism. Biochem Biophys Res Commun 2007; 362:319-24. [PMID: 17716629 DOI: 10.1016/j.bbrc.2007.07.184] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2007] [Accepted: 07/23/2007] [Indexed: 11/27/2022]
Abstract
The crystal structure of Fe-type nitrile hydratase from Rhodococcus erythropolis AJ270 was determined at 1.3A resolution. The two cysteine residues (alphaCys(112) and alphaCys(114)) equatorially coordinated to the ferric ion were post-translationally modified to cysteine sulfinic acids. A glutamine residue (alphaGln(90)) in the active center gave double conformations. Based on the interactions among the enzyme, substrate and water molecules, a new mechanism of biocatalysis of nitrile hydratase was proposed, in which the water molecule activated by the glutamine residue performed as the nucleophile to attack on the nitrile which was simultaneously interacted by another water molecule coordinated to the ferric ion.
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Affiliation(s)
- Liya Song
- State Key Laboratories of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Okamoto S, Eltis LD. Purification and characterization of a novel nitrile hydratase from Rhodococcus sp. RHA1. Mol Microbiol 2007; 65:828-38. [PMID: 17635193 DOI: 10.1111/j.1365-2958.2007.05834.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The microbial degradation of nitriles is of interest for bioremediation and green chemistry. We demonstrated that the soil bacterium Rhodococcus sp. RHA1 utilizes a range of nitriles, including acetonitrile, as growth substrates. Proteomic analysis identified 13 proteins that were more abundant in acetonitrile-grown cells, including an aliphatic amidase and a protein with no known homologue. Purification of a nitrile hydratase (NHase) from acetonitrile-grown cells identified the unknown protein as the beta subunit of a two-subunit NHase. Sequence analysis revealed that the genes encoding the amidase (anhC) and the NHase (anhAB) occur in a 12.8 kbp cluster located on plasmid pRHL2. The anh gene cluster also encodes an acetyl-CoA hydrolase, transcriptional regulators, a putative cobalt transporter and a protein of unknown function. Striking features of the NHase include the amino acid sequence identity (32%) and large size (63 and 56 kDa) of the alpha and beta subunits, as well as the enzyme's metal ion content (one cobalt, two copper and one zinc). The enzyme possessed similar specificities for acetonitrile and propionitrile (k(cat)/K(m) approximately 7 mM(-1) s(-1)) followed by acrylonitrile and butyronitrile. We propose that this acetonitrile hydratase (ANHase) represents the first member of a previously unknown class of NHases.
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Affiliation(s)
- Sachi Okamoto
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
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Arakawa T, Kawano Y, Kataoka S, Katayama Y, Kamiya N, Yohda M, Odaka M. Structure of Thiocyanate Hydrolase: A New Nitrile Hydratase Family Protein with a Novel Five-coordinate Cobalt(III) Center. J Mol Biol 2007; 366:1497-509. [PMID: 17222425 DOI: 10.1016/j.jmb.2006.12.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2006] [Revised: 12/01/2006] [Accepted: 12/05/2006] [Indexed: 10/23/2022]
Abstract
Thiocyanate hydrolase (SCNase) of Thiobacillus thioparus THI115 is a cobalt(III)-containing enzyme catalyzing the degradation of thiocyanate to carbonyl sulfide and ammonia. We determined the crystal structures of the apo- and native SCNases at a resolution of 2.0 A. SCNases in both forms had a conserved hetero-dodecameric structure, (alphabetagamma)(4). Four alphabetagamma hetero-trimers were structurally equivalent. One alphabetagamma hetero-trimer was composed of the core domain and the betaN domain, which was located at the center of the molecule and linked the hetero-trimers with novel quaternary interfaces. In both the apo- and native SCNases, the core domain was structurally conserved between those of iron and cobalt-types of nitrile hydratase (NHase). Native SCNase possessed the post-translationally modified cysteine ligands, gammaCys131-SO(2)H and gammaCys133-SOH like NHases. However, the low-spin cobalt(III) was found to be in the distorted square-pyramidal geometry, which had not been reported before in any protein. The size as well as the electrostatic properties of the substrate-binding pocket was totally different from NHases with respect to the charge distribution and the substrate accessibility, which rationally explains the differences in the substrate preference between SCNase and NHase.
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Affiliation(s)
- Takatoshi Arakawa
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Cowan DA, Cameron RA, Tsekoa TL. Comparative biology of mesophilic and thermophilic nitrile hydratases. ADVANCES IN APPLIED MICROBIOLOGY 2003; 52:123-58. [PMID: 12964242 DOI: 10.1016/s0065-2164(03)01005-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Don A Cowan
- Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
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