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Li SF, Gao YC, Xu HB, Xu CL, Wang YJ, Liu ZQ, Zheng YG. Substrate access tunnel engineering of a Fe-type nitrile hydratase from Pseudomonas fluorescens ZJUT001 for substrate preference adjustment and catalytic performance enhancement. Bioorg Chem 2024; 152:107744. [PMID: 39213799 DOI: 10.1016/j.bioorg.2024.107744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/08/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Substrate access tunnel engineering is a useful strategy for enzyme modification. In this study, we improved the catalytic performance of Fe-type Nitrile hydratase (Fe-type NHase) from Pseudomonas fluorescens ZJUT001 (PfNHase) by mutating residue Q86 at the entrance of the substrate access tunnel. The catalytic activity of the mutant PfNHase-αQ86W towards benzonitrile, 2-cyanopyridine, 3-cyanopyridine, and 4-hydroxybenzonitrile was enhanced by 9.35-, 3.30-, 6.55-, and 2.71-fold, respectively, compared to that of the wild-type PfNHase (PfNHase-WT). In addition, the mutant PfNHase-αQ86W showed a catalytic efficiency (kcat/Km) towards benzonitrile 17.32-fold higher than the PfNHase-WT. Interestingly, the substrate preference of PfNHase-αQ86W shifted from aliphatic nitriles to aromatic nitrile substrates. Our analysis delved into the structural changes that led to this altered substrate preference, highlighting an expanded entrance tunnel region, theenlarged substrate-binding pocket, and the increased hydrophobic interactions between the substrate and enzyme. Molecular dynamic simulations and dynamic cross-correlation Matrix (DCCM) further supported these findings, providing a comprehensive explanation for the enhanced catalytic activity towards aromatic nitrile substrates.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yan-Chi Gao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Hao-Bo Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Cheng-Long Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China.
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
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Rädisch R, Pátek M, Křístková B, Winkler M, Křen V, Martínková L. Metabolism of Aldoximes and Nitriles in Plant-Associated Bacteria and Its Potential in Plant-Bacteria Interactions. Microorganisms 2022; 10:549. [PMID: 35336124 PMCID: PMC8955678 DOI: 10.3390/microorganisms10030549] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/22/2022] Open
Abstract
In plants, aldoximes per se act as defense compounds and are precursors of complex defense compounds such as cyanogenic glucosides and glucosinolates. Bacteria rarely produce aldoximes, but some are able to transform them by aldoxime dehydratase (Oxd), followed by nitrilase (NLase) or nitrile hydratase (NHase) catalyzed transformations. Oxds are often encoded together with NLases or NHases in a single operon, forming the aldoxime-nitrile pathway. Previous reviews have largely focused on the use of Oxds and NLases or NHases in organic synthesis. In contrast, the focus of this review is on the contribution of these enzymes to plant-bacteria interactions. Therefore, we summarize the substrate specificities of the enzymes for plant compounds. We also analyze the taxonomic and ecological distribution of the enzymes. In addition, we discuss their importance in selected plant symbionts. The data show that Oxds, NLases, and NHases are abundant in Actinobacteria and Proteobacteria. The enzymes seem to be important for breaking through plant defenses and utilizing oximes or nitriles as nutrients. They may also contribute, e.g., to the synthesis of the phytohormone indole-3-acetic acid. We conclude that the bacterial and plant metabolism of aldoximes and nitriles may interfere in several ways. However, further in vitro and in vivo studies are needed to better understand this underexplored aspect of plant-bacteria interactions.
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Affiliation(s)
- Robert Rädisch
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Viničná 5, CZ-128 44 Prague, Czech Republic
| | - Miroslav Pátek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Barbora Křístková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
- Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Margit Winkler
- Institute of Molecular Biotechnology, Faculty of Technical Chemistry, Chemical and Process Engineering, Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
- Austrian Center of Industrial Biotechnology GmbH, Krenngasse 37, A-8010 Graz, Austria
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Ludmila Martínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
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Cheng Z, Xia Y, Zhou Z. Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications. Front Bioeng Biotechnol 2020; 8:352. [PMID: 32391348 PMCID: PMC7193024 DOI: 10.3389/fbioe.2020.00352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.
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Affiliation(s)
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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4
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Yu H, Jiao S, Wang M, Liang Y, Tang L. Biodegradation of Nitriles by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Zhang H, Li M, Li J, Wang G, Li F, Xiong M. Chaperone-assisted maturation of the recombinant Fe-type nitrile hydratase is insufficient for fully active expression in Escherichia coli. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Nelp MT, Astashkin AV, Breci LA, McCarty RM, Bandarian V. The alpha subunit of nitrile hydratase is sufficient for catalytic activity and post-translational modification. Biochemistry 2014; 53:3990-4. [PMID: 24914472 PMCID: PMC4075990 DOI: 10.1021/bi500260j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Nitrile hydratases (NHases) possess
a mononuclear iron or cobalt
cofactor whose coordination environment includes rare post-translationally
oxidized cysteine sulfenic and sulfinic acid ligands. This cofactor
is located in the α-subunit at the interfacial active site of
the heterodimeric enzyme. Unlike canonical NHases, toyocamycin nitrile
hydratase (TNHase) from Streptomyces rimosus is a
unique three-subunit member of this family involved in the biosynthesis
of pyrrolopyrimidine antibiotics. The subunits of TNHase are homologous
to the α- and β-subunits of prototypical NHases. Herein
we report the expression, purification, and characterization of the
α-subunit of TNHase. The UV–visible, EPR, and mass spectra
of the α-subunit TNHase provide evidence that this subunit alone
is capable of synthesizing the active site complex with full post-translational
modifications. Remarkably, the isolated post-translationally modified α-subunit
is also catalytically active with the natural substrate, toyocamycin,
as well as the niacin precursor 3-cyanopyridine. Comparisons of the
steady state kinetic parameters of the single subunit variant to the
heterotrimeric protein clearly show that the additional subunits impart
substrate specificity and catalytic efficiency. We conclude that the
α-subunit is the minimal sequence needed for nitrile hydration
providing a simplified scaffold to study the mechanism and post-translational
modification of this important class of catalysts.
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Affiliation(s)
- Micah T Nelp
- Department of Chemistry and Biochemistry, University of Arizona , 1041 E. Lowell Street, Biological Sciences West 540, Tucson, Arizona 85721-0088, United States
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Discovery of a new Fe-type nitrile hydratase efficiently hydrating aliphatic and aromatic nitriles by genome mining. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Addition of Co2+ to culture medium decides the functional expression of a recombinant nitrile hydratase in Escherichia coli. Biotechnol Lett 2013; 35:1419-24. [DOI: 10.1007/s10529-013-1215-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
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10
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Kannan K, Jasra RV. Designing of nitrile hydratase from alkaline protease using quanidine hydrochloride and cobalt metal ion. Catal Today 2012. [DOI: 10.1016/j.cattod.2012.08.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Blaby-Haas CE, Flood JA, Crécy-Lagard VD, Zamble DB. YeiR: a metal-binding GTPase from Escherichia coli involved in metal homeostasis. Metallomics 2012; 4:488-97. [PMID: 22511334 DOI: 10.1039/c2mt20012k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A comparative genomic analysis predicted that many members of the under-characterized COG0523 subfamily of putative P-loop GTPases function in metal metabolism. In this work we focused on the uncharacterized Escherichia coli protein YeiR by studying both the physiology of a yeiR mutant and the in vitro biochemical properties of YeiR expressed as a fusion with the maltose-binding protein (YeiR-MBP). Our results demonstrate that deletion of yeiR increases the sensitivity of E. coli to EDTA or cadmium, and this phenotype is linked to zinc depletion. In vitro, the tagged protein binds several Zn(2+) ions with nanomolar affinity and oligomerizes in the presence of metal. The GTPase activity of YeiR is similar to that measured for other members of the group, but GTP hydrolysis is enhanced by Zn(2+) binding. These results support the predicted connection between the COG0523 P-loop GTPases and roles in metal homeostasis.
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Affiliation(s)
- Crysten E Blaby-Haas
- Department of Microbiology & Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611-0700, USA.
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Synthesis and characterization of an unsymmetrical cobalt(III) active site analogue of nitrile hydratase. J Biol Inorg Chem 2011; 16:937-47. [PMID: 21638158 DOI: 10.1007/s00775-011-0794-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 05/19/2011] [Indexed: 10/18/2022]
Abstract
The design, synthesis, and characterization of an unsymmetrical diamidato-dithiol ligand (H(4) 1, where the hydrogen atoms represent deprotonatable amide and thiol protons) and its cobalt(III) complex, a synthetic analogue of the cobalt-containing nitrile hydratase enzyme family, are reported. The ligand was prepared in 24% yield from an overall eight-step synthetic pathway following a modified protocol established in our laboratory that includes two peptide couples using O-(1H-benzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate as the coupling agent. The ligand and all precursors were characterized by NMR spectroscopy and elemental analysis. The cobalt nitrile hydratase synthetic analogue complex [NBu(4)][Co(1)] was prepared on deprotonating ligand H(4) 1 to [1](4-) on addition of 5 equiv of NaH in N,N-dimethylformamide and adding 1 equiv of CoCl(2) at -40 °C under a N(2) atmosphere followed by oxidizing the complex by stirring it overnight open to dry air. The complex [NBu(4)][Co(1)] was isolated after counterion exchange with 1 equiv of NBu(4)Cl followed by crystallization from MeCN/Et(2)O in 71% yield. The structure of the complex was confirmed by X-ray diffraction analysis. Cyclic voltammetry studies on [NBu(4)][Co(1)] in a 0.1 M [NBu(4)][PF(6)]/MeCN solution showed a quasi-reversible reduction potential at -1.1 V (vs. Ag/AgCl), and magnetic susceptibility investigations indicated the complex is paramagnetic in both the solid and the solution states as determined from inverse-Gouy and Evans NMR methods, respectively.
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Swartz RD, Coggins MK, Kaminsky W, Kovacs JA. Nitrile hydration by thiolate- and alkoxide-ligated Co-NHase analogues. Isolation of Co(III)-amidate and Co(III)-iminol intermediates. J Am Chem Soc 2011; 133:3954-63. [PMID: 21351789 DOI: 10.1021/ja108749f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrile hydratases (NHases) are thiolate-ligated Fe(III)- or Co(III)-containing enzymes, which convert nitriles to the corresponding amide under mild conditions. Proposed NHase mechanisms involve M(III)-NCR, M(III)-OH, M(III)-iminol, and M(III)-amide intermediates. There have been no reported crystallographically characterized examples of these key intermediates. Spectroscopic and kinetic data support the involvement of a M(III)-NCR intermediate. A H-bonding network facilitates this enzymatic reaction. Herein we describe two biomimetic Co(III)-NHase analogues that hydrate MeCN, and four crystallographically characterized NHase intermediate analogues, [Co(III)(S(Me2)N(4)(tren))(MeCN)](2+) (1), [Co(III)(S(Me2)N(4)(tren))(OH)](+) (3), [Co(III)(S(Me2)N(4)(tren))(NHC(O)CH(3))](+) (2), and [Co(III)(O(Me2)N(4)(tren))(NHC(OH)CH(3))](2+) (5). Iminol-bound 5 represents the first example of a Co(III)-iminol compound in any ligand environment. Kinetic parameters (k(1)(298 K) = 2.98(5) M(-1) s(-1), ΔH(‡) = 12.65(3) kcal/mol, ΔS(‡) = -14(7) e.u.) for nitrile hydration by 1 are reported, and the activation energy E(a) = 13.2 kcal/mol is compared with that (E(a) = 5.5 kcal/mol) of the NHase enzyme. A mechanism involving initial exchange of the bound MeCN for OH- is ruled out by the fact that nitrile exchange from 1 (k(ex)(300 K) = 7.3(1) × 10(-3) s(-1)) is 2 orders of magnitude slower than nitrile hydration, and that hydroxide bound 3 does not promote nitrile hydration. Reactivity of an analogue that incorporates an alkoxide as a mimic of the highly conserved NHase serine residue shows that this moiety facilitates nitrile hydration under milder conditions. Hydrogen-bonding to the alkoxide stabilizes a Co(III)-iminol intermediate. Comparison of the thiolate versus alkoxide intermediate structures shows that C≡N bond activation and C═O bond formation proceed further along the reaction coordinate when a thiolate is incorporated into the coordination sphere.
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Affiliation(s)
- Rodney D Swartz
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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15
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Nitrile hydratases (NHases): At the interface of academia and industry. Biotechnol Adv 2010; 28:725-41. [DOI: 10.1016/j.biotechadv.2010.05.020] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 11/19/2022]
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Zhou Z, Hashimoto Y, Cui T, Washizawa Y, Mino H, Kobayashi M. Unique Biogenesis of High-Molecular Mass Multimeric Metalloenzyme Nitrile Hydratase: Intermediates and a Proposed Mechanism for Self-Subunit Swapping Maturation. Biochemistry 2010; 49:9638-48. [DOI: 10.1021/bi100651v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhemin Zhou
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yoshiteru Hashimoto
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Tianwei Cui
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yumi Washizawa
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroyuki Mino
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Coffey L, Owens E, Tambling K, O'Neill D, O'Connor L, O'Reilly C. Real-time PCR detection of Fe-type nitrile hydratase genes from environmental isolates suggests horizontal gene transfer between multiple genera. Antonie van Leeuwenhoek 2010; 98:455-63. [PMID: 20502965 DOI: 10.1007/s10482-010-9459-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 05/14/2010] [Indexed: 11/25/2022]
Abstract
Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.
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Affiliation(s)
- Lee Coffey
- Pharmaceutical & Molecular Biotechnology Research Centre, Chemical & Life Sciences Department, Waterford Institute of Technology, Ireland.
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Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, de Crécy-Lagard V. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics 2009; 10:470. [PMID: 19822009 PMCID: PMC2770081 DOI: 10.1186/1471-2164-10-470] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 10/12/2009] [Indexed: 11/11/2022] Open
Abstract
Background COG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first COG0523-encoding gene, cobW, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. Results Based on a combination of comparative genomics, literature and phylogenetic analyses and experimental validations, the COG0523 family can be separated into at least fifteen subgroups. The CobW subgroup involved in cobalamin synthesis represents only one small sub-fraction of the family. Another, larger subgroup, is suggested to play a predominant role in the response to zinc limitation based on the presence of the corresponding COG0523-encoding genes downstream from putative Zur binding sites in many bacterial genomes. Zur binding sites in these genomes are also associated with candidate zinc-independent paralogs of zinc-dependent enzymes. Finally, the potential role of COG0523 in zinc homeostasis is not limited to Bacteria. We have predicted a link between COG0523 and regulation by zinc in Archaea and show that two COG0523 genes are induced upon zinc depletion in a eukaryotic reference organism, Chlamydomonas reinhardtii. Conclusion This work lays the foundation for the pursuit by experimental methods of the specific role of COG0523 members in metal trafficking. Based on phylogeny and comparative genomics, both the metal specificity and the protein target(s) might vary from one COG0523 subgroup to another. Additionally, Zur-dependent expression of COG0523 and putative paralogs of zinc-dependent proteins may represent a mechanism for hierarchal zinc distribution and zinc sparing in the face of inadequate zinc nutrition.
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Affiliation(s)
- Crysten E Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
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Discovery of posttranslational maturation by self-subunit swapping. Proc Natl Acad Sci U S A 2008; 105:14849-54. [PMID: 18809911 DOI: 10.1073/pnas.0803428105] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several general mechanisms of metallocenter biosynthesis have been reported and reviewed, and in all cases, the components or subunits of an apoprotein remain in the final holoprotein. Here, we first discovered that one subunit of an apoenzyme did not remain in the functional holoenzyme. The cobalt-containing low-molecular-mass nitrile hydratase (L-NHase) of Rhodococcus rhodochrous J1 consists of beta- and alpha-subunits encoded by the nhlBA genes, respectively. An ORF, nhlE, just downstream of nhlBA, was found to be necessary for L-NHase activation. In contrast to the cobalt-containing L-NHase (holo-L-NHase containing Cys-SO(2)(-) and Cys-SO(-) metal ligands) derived from nhlBAE, the gene products derived from nhlBA were cobalt-free L-NHase (apo-L-NHase lacking oxidized cysteine residues). We discovered an L-NHase maturation mediator, NhlAE, consisting of NhlE and the cobalt- and oxidized cysteine-containing alpha-subunit of L-NHase. The incorporation of cobalt into L-NHase was shown to depend on the exchange of the nonmodified cobalt-free alpha-subunit of apo-L-NHase with the cobalt-containing cysteine-modified alpha-subunit of NhlAE. This is a posttranslational maturation process different from general mechanisms of metallocenter biosynthesis known so far: the unexpected behavior of a protein in a protein complex, which we named "self-subunit swapping."
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Bezsudnova EY, Sorokin DY, Tikhonova TV, Popov VO. Thiocyanate hydrolase, the primary enzyme initiating thiocyanate degradation in the novel obligately chemolithoautotrophic halophilic sulfur-oxidizing bacterium Thiohalophilus thiocyanoxidans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1563-70. [PMID: 17964868 DOI: 10.1016/j.bbapap.2007.09.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 09/12/2007] [Accepted: 09/12/2007] [Indexed: 11/17/2022]
Abstract
Thiohalophilus thiocyanoxidans is a first halophilic sulfur-oxidizing chemolithoautotrophic bacterium capable of growth with thiocyanate as an electron donor at salinity up to 4 M NaCl. The cells, grown with thiocyanate, but not with thiosulfate, contained an enzyme complex hydrolyzing thiocyanate to sulfide and ammonia under anaerobic conditions with carbonyl sulfide as an intermediate. Despite the fact of utilization of the <<COS pathway>>, high cyanase activity was also detected in thiocyanate-induced cells. Three-stage column chromotography resulted in a highly purified thiocyanate-hydrolyzing protein with an apparent molecular mass of 140 kDa that consists of three subunits with masses 17, 19 and 29 kDa. The enzyme is a Co,Fe-containing protein resembling on its function and subunit composition the enzyme thiocyanate hydrolase from the Betaproteobacterium Thiobacillus thioparus. Cyanase, copurified with thiocyanate hydrolase, is a bisubstrate multisubunit enzyme with an apparent subunit molecular mass of 14 kDa. A possible role of cyanase in thiocyanate degradation by T. thiocyanoxidans is discussed.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia.
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21
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WANG C, ZHANG G, XU X, LI C. Inducing Expression and Reaction Characteristic of Nitrile Hydratase from Rhodococcus sp. SHZ-1. Chin J Chem Eng 2007. [DOI: 10.1016/s1004-9541(07)60126-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Sari MA, Jaouen M, Saroja NR, Artaud I. Influence of cobalt substitution on the activity of iron-type nitrile hydratase: are cobalt type nitrile hydratases regulated by carbon monoxide? J Inorg Biochem 2006; 101:614-22. [PMID: 17267045 DOI: 10.1016/j.jinorgbio.2006.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 12/07/2006] [Accepted: 12/08/2006] [Indexed: 11/15/2022]
Abstract
Comamonas testosteroni Ni1 nitrile hydratase is a Fe-type nitrile hydratase whose native and recombinant forms are identical. Here, the iron of Ni1 nitrile hydratase was replaced by cobalt using a chaperone based Escherichia coli expression system. Cobalt (CoNi1) and iron (FeNi1) enzymes share identical Vmax (30 nmol min(-1) mg(-1)) and Km (200 microM) toward their substrate and identical Ki values for the known competitive inhibitors of FeNi1. However, nitrophenols used as inhibitors do display a different inhibition pattern on both enzymes. Furthermore, CoNi1 and FeNi1 are also different in their sensitivity to nitric oxide and carbon monoxide, CO being selective of the cobalt enzyme. These differences are rationalized in relation to the nature of the catalytic metal center in the enzyme.
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Affiliation(s)
- Marie-Agnès Sari
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, UMR 8601 CNRS, 45 Rue des Saint-Pères, 75270 Paris Cedex 06, France.
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23
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Greene SN, Richards NGJ. Electronic structure, bonding, spectroscopy and energetics of Fe-dependent nitrile hydratase active-site models. Inorg Chem 2006; 45:17-36. [PMID: 16390037 DOI: 10.1021/ic050965p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fe-type nitrile hydratase (NHase) is a non-heme Fe(III)-dependent enzyme that catalyzes the hydration of nitriles to the corresponding amides. Despite experimental studies of the enzyme and model Fe(III)-containing complexes, many questions concerning the electronic structure and spectroscopic transitions of the metal center remain unanswered. In addition, the catalytic mechanism of nitrile hydration has not yet been determined. We now report density functional theory (B3LYP/6-31G) calculations on three models of the Fe(III) center in the active site of NHase corresponding to hypothetical intermediates in the enzyme-catalyzed hydration of acetonitrile. Together with natural bond orbital (NBO) analysis of the chemical bonding in these active-site models and INDO/S CIS calculations of their electronic spectra, this theoretical investigation gives new insight into the molecular origin of the unusual low-spin preference and spectroscopic properties of the Fe(III) center. In addition, the low-energy electronic transition observed for the active form of NHase is assigned to a dd transition that is coupled with charge-transfer transitions involving the metal and its sulfur ligands. Calculations of isodesmic ligand-exchange reaction energies provide support for coordination of the Fe(III) center in free NHase by a water molecule rather than a hydroxide ion and suggest that the activation of the nitrile substrate by binding to the metal in the sixth coordination site during catalytic turnover cannot yet be definitively ruled out.
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Affiliation(s)
- Shannon N Greene
- Department of Chemistry, University of Florida, Gainesville, 32611-7200, USA
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24
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Katayama Y, Hashimoto K, Nakayama H, Mino H, Nojiri M, Ono TA, Nyunoya H, Yohda M, Takio K, Odaka M. Thiocyanate Hydrolase Is a Cobalt-Containing Metalloenzyme with a Cysteine-Sulfinic Acid Ligand. J Am Chem Soc 2005; 128:728-9. [PMID: 16417356 DOI: 10.1021/ja057010q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiocyanate hydrolase (SCNase) purified from Thiobacillus thioparus THI115 hydrolyzes thiocyanate to carbonyl sulfide and ammonia. DNA sequences of the cloned genes revealed the close relation of SCNase to nitrile hydratase (NHase). The consensus sequences for coordination of the metal ion found in NHases were also conserved in the gamma subunit of SCNase. Here, we showed that the SCNase contained one cobalt atom per alphabetagamma heterotrimer. UV-vis absorption spectrum suggested that the cobalt exists as a non-corrin ion. Reduced SCNase showed an ESR signal characteristic of low-spin Co2+, which closely resembled that of the Co-type NHases. Mass spectrometry for the peptide fragment containing the metal-binding motif of the SCNase gamma subunit indicated that the cysteine residue at position 131 was post-translationally oxidized to a cysteine-sulfinic acid. From these results, we concluded that SCNases and NHases form a novel non-corrin and/or non-heme protein family having post-translationally modified cysteine ligands.
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Affiliation(s)
- Yoko Katayama
- Department of Environmental and Natural Resource Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
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25
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Cameron RA, Sayed M, Cowan DA. Molecular analysis of the nitrile catabolism operon of the thermophile Bacillus pallidus RAPc8. Biochim Biophys Acta Gen Subj 2005; 1725:35-46. [PMID: 15955632 DOI: 10.1016/j.bbagen.2005.03.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 03/24/2005] [Accepted: 03/28/2005] [Indexed: 11/19/2022]
Abstract
The gene cluster containing the nitrile hydratase (NHase) and amidase genes of a moderate thermophile, B. pallidus RAPc8 has been cloned and sequenced. The (5.9 kb) section of cloned DNA contained eight complete open reading frames, encoding (in order), amidase (belonging to the nitrilase related aliphatic amidase family), nitrile hydratase beta and alpha subunits (of the cobalt containing class), a 122-amino acid accessory protein, designated P14K, a homologue of the 2Fe-2S class of ferredoxins and three putative proteins with distinct homology to the cobalt uptake proteins cbiM, cbiN and cbiQ of the S. typhimurium LT2 cobalamin biosynthesis pathway. The amidase and nitrile hydratase genes were subcloned and inducibly expressed in Escherichia coli, to levels of approximately 37 U/mg and 49 U/mg, respectively, without the co-expression of additional flanking genes. However, co-expression of P14K with the NHase structural genes significantly enhanced the specific activity of the recombinant NHase. This is the first description of an accessory protein involved in thermostable NHase expression. Modelling of the P14K protein structure has suggested that this protein functions as a subunit-specific chaperone, aiding in the folding of the NHase alpha subunit prior to alpha-beta subunit association and the formation of alpha(2)beta(2) NHase holoenzyme.
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Affiliation(s)
- Rory A Cameron
- Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
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26
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Bis-axial cyanide coordination induces high nucleophilicity of the in-plane thiolato ligands bound to a Co(III) center: model complexes related to the Co-containing nitrile hydratases. Inorganica Chim Acta 2004. [DOI: 10.1016/j.ica.2004.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Kovacs JA. Synthetic analogues of cysteinate-ligated non-heme iron and non-corrinoid cobalt enzymes. Chem Rev 2004; 104:825-48. [PMID: 14871143 PMCID: PMC4487544 DOI: 10.1021/cr020619e] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julie A Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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28
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Miyanaga A, Fushinobu S, Ito K, Shoun H, Wakagi T. Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding. ACTA ACUST UNITED AC 2004; 271:429-38. [PMID: 14717710 DOI: 10.1046/j.1432-1033.2003.03943.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutants of a cobalt-containing nitrile hydratase (NHase, EC 4.2.1.84) from Pseudonocardia thermophila JCM 3095 involved in substrate binding, catalysis and formation of the active center were constructed, and their characteristics and crystal structures were investigated. As expected from the structure of the substrate binding pocket, the wild-type enzyme showed significantly lower K(m) and K(i) values for aromatic substrates and inhibitors, respectively, than aliphatic ones. In the crystal structure of a complex with an inhibitor (n-butyric acid) the hydroxyl group of betaTyr68 formed hydrogen bonds with both n-butyric acid and alphaSer112, which is located in the active center. The betaY68F mutant showed an elevated K(m) value and a significantly decreased k(cat) value. The apoenzyme, which contains no detectable cobalt atom, was prepared from Escherichia coli cells grown in medium without cobalt ions. It showed no detectable activity. A disulfide bond between alphaCys108 and alphaCys113 was formed in the apoenzyme structure. In the highly conserved sequence motif in the cysteine cluster region, two positions are exclusively conserved in cobalt-containing or iron-containing nitrile hydratases. Two mutants (alphaT109S and alphaY114T) were constructed, each residue being replaced with an iron-containing one. The alphaT109S mutant showed similar characteristics to the wild-type enzyme. However, the alphaY114T mutant showed a very low cobalt content and catalytic activity compared with the wild-type enzyme, and oxidative modifications of alphaCys111 and alphaCys113 residues were not observed. The alphaTyr114 residue may be involved in the interaction with the nitrile hydratase activator protein of P. thermophila.
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29
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Lu J, Zheng Y, Yamagishi H, Odaka M, Tsujimura M, Maeda M, Endo I. Motif CXCC in nitrile hydratase activator is critical for NHase biogenesis in vivo. FEBS Lett 2003; 553:391-6. [PMID: 14572657 DOI: 10.1016/s0014-5793(03)01070-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nitrile hydratase (NHase) activator from Rhodococcus sp. N-771 is required for NHase functional expression. The motif 73CXCC76 in the NHase activator sequence was here revealed to be vital for its function by site-directed mutagenesis. All three substitutions of the cysteines by serines resulted in a much lower level of expression of active NHase. Furthermore, interaction between NHase activator and NHase was detected and the critical role of NHase activator was not exhibited in the cysteine oxidization process of NHase. These findings suggest NHase activator mainly participates in iron trafficking in NHase biogenesis as an iron type metallochaperone.
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Affiliation(s)
- Jun Lu
- The Institute of Physical and Chemical Research, Wako Shi, 351-0198 Saitama, Japan.
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30
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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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31
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Noguchi T, Nojiri M, Takei KI, Odaka M, Kamiya N. Protonation Structures of Cys-Sulfinic and Cys-Sulfenic Acids in the Photosensitive Nitrile Hydratase Revealed by Fourier Transform Infrared Spectroscopy†. Biochemistry 2003; 42:11642-50. [PMID: 14529274 DOI: 10.1021/bi035260i] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrile hydratase (NHase) from Rhodococcus N-771, which catalyzes hydration of nitriles to the corresponding amides, exhibits novel photosensitivity; in the dark, it is in the inactive form that binds an endogenous nitric oxide (NO) molecule at the non-heme iron center, and photodissociation of the NO activates the enzyme. NHase is also known to have a unique active site structure. Two cysteine ligands to the iron center, alphaCys112 and alphaCys114, are post-translationally modified to sulfinic acid (Cys-SO(2)H) and sulfenic acid (Cys-SOH), respectively, which are thought to play a crucial role in the catalytic reaction. Here, we have determined the protonation structures of these Cys-SO(2)H and Cys-SOH groups using Fourier transform infrared (FTIR) spectroscopy in combination with density functional theory (DFT) calculations. The light-induced FTIR difference spectrum of NHase between the dark inactive and light active forms exhibited two prominent signals at (1154-1148)/1126 and (1040-1034)/1019 cm(-1), which downshifted to 1141/1114 and 1026/1012 cm(-1), respectively, in the uniformly (34)S-labeled NHase. In addition, a minor signal at 915/908 cm(-1) also showed a considerable downshift upon (34)S labeling. These (34)S-sensitive signals were basically conserved in D(2)O buffer with only slight shifts. Vibrational frequencies of methanesulfenic acid (CH(3)SOH) and methanesulfinic acid (CH(3)SO(2)H), simple model compounds of Cys-SOH and Cys-SO(2)H, respectively, were calculated using the DFT method in both the protonated and deprotonated forms and in metal complexes. Comparison of the calculated frequencies and isotope shifts with the observed ones provided the assignment of the two major signals around 1140 and 1030 cm(-1) to the asymmetric and symmetric SO(2) stretching vibrations, respectively, of the S-bonded Cys-SO(2)(-) complex, and the assignment of the minor signal around 910 cm(-1) most likely to the SO stretch of the S-bonded Cys-SO(-) complex. These assignments and the small frequency shifts upon deuteration are consistent with the view that the deprotonated alphaCys112-SO(2)(-) and alphaCys114-SO(-) are hydrogen-bonded with the protons from betaArg56 and/or betaArg141, forming a reactive cavity at the interface of the alpha and beta subunits. There is further speculation that either of these groups is hydrogen bonded to a reactant water molecule, increasing its basicity to facilitate the nucleophilic attack on the nitrile substrate bound to the iron center.
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Affiliation(s)
- Takumi Noguchi
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan.
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32
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Tsujimura M, Odaka M, Nakayama H, Dohmae N, Koshino H, Asami T, Hoshino M, Takio K, Yoshida S, Maeda M, Endo I. A novel inhibitor for Fe-type nitrile hydratase: 2-cyano-2-propyl hydroperoxide. J Am Chem Soc 2003; 125:11532-8. [PMID: 13129355 DOI: 10.1021/ja035018z] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrile hydratase (NHase) is a non-heme iron or non-corrin cobalt enzyme having two post-translationally modified ligand residues, cysteine-sulfinic acid (alphaCys112-SO(2)H) and -sulfenic acid (alphaCys114-SOH). We studied the interaction between Fe-type NHase and isobutyronitrile (iso-BN) which had been reported as a competitive inhibitor with a K(i) value of 5 microM. From detailed kinetic studies of the inhibitory effect of iso-BN on Fe-type NHase, we found that authentic iso-BN was hydrated normally and that the impurity present in commercially available iso-BN inhibited NHase activity strongly. The inhibitory compound induced significant changes in the UV-vis absorption spectrum of NHase, suggesting its interaction with the iron center. This compound was purified by using reversed-phase HPLC and identified as 2-cyano-2-propyl hydroperoxide (Cpx) by (1)H and PFG-HMBC NMR spectroscopy. Upon addition of a stoichiometric amount of Cpx, NHase was irreversibly inactivated, probably by the oxidation of alphaCys114-SOH to Cys-SO(2)H. This result suggests that the -SOH structure of alphaCys114 is essential for the catalytic activity. The oxygen atom in Cys-SO(2)H is confirmed to come from the solvent H(2)O. The oxidized NHase was found to induce the UV-vis absorption spectral changes by addition of Cpx, suggesting that Cpx strongly interacted with iron(III) in the oxidized NHase to form a stable complex. Thus, Cpx functions as a novel irreversible inhibitor for NHase.
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Affiliation(s)
- Masanari Tsujimura
- Biomolecular Characterization Division, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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33
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Tyler LA, Noveron JC, Olmstead MM, Mascharak PK. Modulation of the pK(a) of metal-bound water via oxidation of thiolato sulfur in model complexes of Co(III) containing nitrile hydratase: insight into possible effect of cysteine oxidation in Co-nitrile hydratase. Inorg Chem 2003; 42:5751-61. [PMID: 12950226 DOI: 10.1021/ic030088s] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Co(III) complexes of N,N'-bis(2-mercaptophenyl)pyridine-2,6-dicarboxamide (PyPSH(4)), a designed pentadentate ligand with built-in carboxamide and thiolate groups, have been synthesized and studied to gain insight into the role of Cys-S oxidation in Co-containing nitrile hydratase (Co-NHase). Reaction of [Co(NH(3))(5)Cl]Cl(2) with PyPS(4)(-) in DMF affords the thiolato-bridged dimeric Co(III) complex (Et(4)N)(2)[Co(2)(PyPS)(2)] (1). Although the bridged structure is quite robust, reaction of (Et(4)N)(CN) with 1 in acetonitrile affords the monomeric species (Et(4)N)(2)[Co(PyPS)(CN)] (2). Oxidation of 2 with H(2)O(2) in acetonitrile gives rise to a mixture which, upon chromatographic purification, yields K(2)[Co(PyPSO(2)(OSO(2))(CN] (3), a species containing asymmetrically oxidized thiolates. The Co(III) metal center in 3 is coordinated to a S-bound sulfinate and an O-bound sulfonate (OSO(2)) group. Upon oxidation with H(2)O(2), 1 affords an asymmetrically oxidized dimer (Et(4)N)(2)[Co(2)(PyPS(SO(2)))(2)] (4) in which only the terminal thiolates are oxidized to form S-bound sulfinate groups while the bridging thiolates remain unchanged. The thiolato-bridge in 4 is also cleaved upon reaction with (Et(4)N)(CN) in acetonitrile, and one obtains (Et(4)N)(2)[Co(PyPS(SO(2)))(CN)] (5), a species that contains both coordinated thiolate and S-bound sulfinate around Co(III). The structures of 1-4 have been determined. The spectroscopic properties and reactivity of all the complexes have been studied to understand the behavior of the Co(III) site in Co-NHase. Unlike typical Co(III) complexes with bound CN(-) ligands, the Co(III) centers in 2 and 5 are labile and rapidly lose CN(-) in aqueous solutions. Since 3 does not show this lability, it appears that at least one thiolato sulfur donor is required in the first coordination sphere for the Co(III) center in such species to exhibit lability. Both 2 and 5 are converted to the aqua complexes [Co(PyPS)(H(2)O)](-) and [Co(PyPS(SO(2))(H(2)O)](-) in aqueous solutions. The pK(a) values of the bound water in these two species, determined by spectrophotometry, are 8.3 +/- 0.03 and 7.2 +/- 0.06, respectively. Oxidation of the thiolato sulfur (to sulfinate) therefore increases the acidity of the bound water. Since 2 and 5 promote hydrolysis of acetonitrile at pH values above their corresponding pK(a) values, it is also evident that a metal-bound hydroxide is a key player in the mechanism of hydrolysis by these model complexes of Co-NHase. The required presence of a Cys-sulfinic residue and one water molecule at the Co(III) site of Co-NHase as well as the optimal pH of the enzyme near 7 suggests that (i) modulation of the pK(a) of the bound water molecule at the active site of the enzyme could be one role of the oxidized Cys-S residue(s) and (ii) a cobalt-bound hydroxide could be responsible for the hydrolysis of nitriles by Co-NHase.
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Affiliation(s)
- Laurie A Tyler
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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34
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Shearer J, Jackson HL, Schweitzer D, Rittenberg DK, Leavy TM, Kaminsky W, Scarrow RC, Kovacs JA. The first example of a nitrile hydratase model complex that reversibly binds nitriles. J Am Chem Soc 2002; 124:11417-28. [PMID: 12236756 PMCID: PMC4485622 DOI: 10.1021/ja012555f] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitrile hydratase (NHase) is an iron-containing metalloenzyme that converts nitriles to amides. The mechanism by which this biochemical reaction occurs is unknown. One mechanism that has been proposed involves nucleophilic attack of an Fe-bound nitrile by water (or hydroxide). Reported herein is a five-coordinate model compound ([Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+)) containing Fe(III) in an environment resembling that of NHase, which reversibly binds a variety of nitriles, alcohols, amines, and thiocyanate. XAS shows that five-coordinate [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) reacts with both methanol and acetonitrile to afford a six-coordinate solvent-bound complex. Competitive binding studies demonstrate that MeCN preferentially binds over ROH, suggesting that nitriles would be capable of displacing the H(2)O coordinated to the iron site of NHase. Thermodynamic parameters were determined for acetonitrile (DeltaH = -6.2(+/-0.2) kcal/mol, DeltaS = -29.4(+/-0.8) eu), benzonitrile (-4.2(+/-0.6) kcal/mol, DeltaS = -18(+/-3) eu), and pyridine (DeltaH = -8(+/-1) kcal/mol, DeltaS = -41(+/-6) eu) binding to [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) using variable-temperature electronic absorption spectroscopy. Ligand exchange kinetics were examined for acetonitrile, iso-propylnitrile, benzonitrile, and 4-tert-butylpyridine using (13)C NMR line-broadening analysis, at a variety of temperatures. Activation parameters for ligand exchange were determined to be DeltaH(+ +) = 7.1(+/-0.8) kcal/mol, DeltaS(+ +) = -10(+/-1) eu (acetonitrile), DeltaH(+ +) = 5.4(+/-0.6) kcal/mol, DeltaS(+ +) = -17(+/-2) eu (iso-propionitrile), DeltaH(+ +) = 4.9(+/-0.8) kcal/mol, DeltaS(+ +) = -20(+/-3) eu (benzonitrile), and DeltaH(+ +) = 4.7(+/-1.4) kcal/mol DeltaS(+ +) = -18(+/-2) eu (4-tert-butylpyridine). The thermodynamic parameters for pyridine binding to a related complex, [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))](+) (DeltaH = -5.9(+/-0.8) kcal/mol, DeltaS = -24(+/-3) eu), are also reported, as well as kinetic parameters for 4-tert-butylpyridine exchange (DeltaH(+ +) = 3.1(+/-0.8) kcal/mol, DeltaS(+ +) = -25(+/-3) eu). These data show for the first time that, when it is contained in a ligand environment similar to that of NHase, Fe(III) is capable of forming a stable complex with nitriles. Also, the rates of ligand exchange demonstrate that low-spin Fe(III) in this ligand environment is more labile than expected. Furthermore, comparison of [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) and [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))](+) demonstrates how minor distortions induced by ligand constraints can dramatically alter the reactivity of a metal complex.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Henry L. Jackson
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Dirk Schweitzer
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Durrell K. Rittenberg
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Tanya M. Leavy
- Department of Chemistry, Haverford College, Haverford, PennsylVania 19041
| | | | - Robert C. Scarrow
- Department of Chemistry, Haverford College, Haverford, PennsylVania 19041
| | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
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35
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Miyanaga A, Fushinobu S, Ito K, Wakagi T. Crystal structure of cobalt-containing nitrile hydratase. Biochem Biophys Res Commun 2001; 288:1169-74. [PMID: 11700034 DOI: 10.1006/bbrc.2001.5897] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structure of cobalt-containing nitrile hydratase from Pseudonocardia thermophila JCM 3095 at 1.8 A resolution revealed the structure of the noncorrin cobalt at the catalytic center. Two cysteine residues (alphaCys(111) and alphaCys(113)) coordinated to the cobalt were posttranslationally modified to cysteine-sulfinic acid and to cysteine-sulfenic acid, respectively, like in iron-containing nitrile hydratase. A tryptophan residue (betaTrp(72)), which may be involved in substrate binding, replaced the tyrosine residue of iron-containing nitrile hydratase. The difference seems to be responsible for the preference for aromatic nitriles rather than aliphatic ones of cobalt-containing nitrile hydratase.
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Affiliation(s)
- A Miyanaga
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Heinrich L, Mary-Verla A, Li Y, Vaissermann J, Chottard JC. Cobalt(III) Complexes with Carboxamido-N and Sulfenato-S or Sulfinato-S Ligands Suggest that a Coordinated Sulfenate-S is Essential for the Catalytic Activity of Nitrile Hydratases. Eur J Inorg Chem 2001. [DOI: 10.1002/1099-0682(200109)2001:9<2203::aid-ejic2203>3.0.co;2-a] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Endo I, Nojiri M, Tsujimura M, Nakasako M, Nagashima S, Yohda M, Odaka M. Fe-type nitrile hydratase. J Inorg Biochem 2001; 83:247-53. [PMID: 11293544 DOI: 10.1016/s0162-0134(00)00171-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The characteristic features of Fe-type nitrile hydratase (NHase) from Rhodococcus sp. N-771 are described. Through the biochemical analyses, we have found that nitric oxide (NO) regulates the photoreactivity of this enzyme by association with the non-heme iron center and photoinduced dissociation from it. The regulation is realized by a unique structure of the catalytic non-heme iron center composed of post-translationally modified cysteine-sulfinic (Cys-SO2H) and -sulfenic acids (Cys-SOH). To understand the biogenic mechanism and the functional role of these modifications, we constructed an over-expression system of whole NHase and individual subunits in Escherichia coli. The results of the studies on several recombinant NHases have shown that the Cys-SO2H oxidation of alphaC112 is indispensable for the catalytic activity of Fe-type NHase.
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Affiliation(s)
- I Endo
- Biochemical Systems Laboratory, The Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama, Japan.
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Shearer J, Kung IY, Lovell S, Kaminsky W, Kovacs JA. Why is there an "inert" metal center in the active site of nitrile hydratase? Reactivity and ligand dissociation from a five-coordinate Co(III) nitrile hydratase model. J Am Chem Soc 2001; 123:463-8. [PMID: 11456548 PMCID: PMC4484831 DOI: 10.1021/ja002642s] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To determine how a substitutionally inert metal can play a catalytic role in the metalloenzyme nitrile hydratase (NHase), a reactive five-coordinate Co(III) thiolate complex ([Co(III)(S(2)(Me2)N(3)(Pr,Pr))](PF(6)) (1)) that resembles the active site of cobalt containing nitrile hydratase (Co NHase) was prepared. This was screened for reactivity, by using low-temperature electronic absorption spectroscopy, toward a number of biologically relevant "substrates". It was determined 1 will react with azide, thiocyanate, and ammonia, but is unreactive toward nitriles, NO, and butyrate. Substrate-bound 1 has similar spectroscopic and structural properties as [Co(III)(ADIT(2))](PF(6)) (2). Complex 2 is a six-coordinate Co(III) complex containing cis-thiolates and imine nitrogens, and has properties similar to the cobalt center of Co NHase. Substrate binding to 1 is reversible and temperature-dependent, allowing for the determination of the thermodynamic parameters of azide and thiocyanate binding and the rates of ligand dissociation. Azide and thiocyanate bind trans to a thiolate, and with similar entropies and enthalpies (thiocyanate: DeltaH = -7.5 +/- 1.1 kcal/mol, DeltaS = -17.2 +/- 3.2 eu; azide: DeltaH = -6.5 +/- 1.0 kcal/mol, DeltaS = -12.6 +/- 2.4 eu). The rates of azide and thiocyanate displacement from the metal center are also comparable to one another (k(d) = (7.22 +/- 0.04) x 10(-)(1) s(-)(1) for thiocyanate and k(d) = (2.14 +/- 0.50) x 10(-)(2) s(-)(1) for azide), and are considerably faster than one would expect for a low-spin d(6) six-coordinate Co(III) complex. These rates are comparable to those of an analogous Fe(III) complex, demonstrating that Co(III) and Fe(III) react at comparable rates when in this ligand environment. This study therefore indicates that ligand displacement from a low-spin Co(III) center in a ligand environment that resembles NHase is not prohibitively slow so as to disallow catalytic action in nonredox active cobalt metalloenzymes.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Irene Y. Kung
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Scott Lovell
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Werner Kaminsky
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Seattle, Washington 98195
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Piersma SR, Nojiri M, Tsujimura M, Noguchi T, Odaka M, Yohda M, Inoue Y, Endo I. Arginine 56 mutation in the beta subunit of nitrile hydratase: importance of hydrogen bonding to the non-heme iron center. J Inorg Biochem 2000; 80:283-8. [PMID: 11001100 DOI: 10.1016/s0162-0134(00)00076-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Arginine 56 in the beta subunit (betaArg56) of the iron-containing nitrile hydratase (NHase), one of the strongly conserved residues within the NHase family, is known to form hydrogen bonds to the sulfinyl (-SO2H) and sulfenyl (-SOH) groups of the post-translationally modified cysteine residues in the catalytic center. BetaArg56 was substituted by tyrosine, glutamate or lysine, respectively, and the respective mutant enzymes generated by reconstitution were characterized. The betaR56K mutant complex exhibited about 1% of the enzymatic activity of native NHase, while the others were totally inactive. The kinetic analysis of the betaR56K mutant complex exhibited a drastic decrease in turnover number and decreases in kinetic constants for substrate and inhibitors as compared to the native NHase. Changes in UV-visible absorption and light-induced Fourier transform infrared difference spectra suggest that betaArg56 is involved in the positioning of the -SO2H and -SOH groups of the modified Cys residues in the catalytic center so as to fine tune the electronic state of the iron center suitable for catalysis. Thus, betaArg56 is essential for catalysis.
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Affiliation(s)
- S R Piersma
- Biochemical Systems Laboratory, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama, Japan
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