1
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Schmidt A, Kalms J, Lorent C, Katz S, Frielingsdorf S, Evans RM, Fritsch J, Siebert E, Teutloff C, Armstrong FA, Zebger I, Lenz O, Scheerer P. Stepwise conversion of the Cys 6[4Fe-3S] to a Cys 4[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase. Chem Sci 2023; 14:11105-11120. [PMID: 37860641 PMCID: PMC10583674 DOI: 10.1039/d3sc03739h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
The membrane-bound [NiFe]-hydrogenase of Cupriavidus necator is a rare example of a truly O2-tolerant hydrogenase. It catalyzes the oxidation of H2 into 2e- and 2H+ in the presence of high O2 concentrations. This characteristic trait is intimately linked to the unique Cys6[4Fe-3S] cluster located in the proximal position to the catalytic center and coordinated by six cysteine residues. Two of these cysteines play an essential role in redox-dependent cluster plasticity, which bestows the cofactor with the capacity to mediate two redox transitions at physiological potentials. Here, we investigated the individual roles of the two additional cysteines by replacing them individually as well as simultaneously with glycine. The crystal structures of the corresponding MBH variants revealed the presence of Cys5[4Fe-4S] or Cys4[4Fe-4S] clusters of different architecture. The protein X-ray crystallography results were correlated with accompanying biochemical, spectroscopic and electrochemical data. The exchanges resulted in a diminished O2 tolerance of all MBH variants, which was attributed to the fact that the modified proximal clusters mediated only one redox transition. The previously proposed O2 protection mechanism that detoxifies O2 to H2O using four protons and four electrons supplied by the cofactor infrastructure, is extended by our results, which suggest efficient shutdown of enzyme function by formation of a hydroxy ligand in the active site that protects the enzyme from O2 binding under electron-deficient conditions.
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Affiliation(s)
- Andrea Schmidt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
| | - Jacqueline Kalms
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Stefan Frielingsdorf
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Johannes Fritsch
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Elisabeth Siebert
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
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2
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Imanishi T, Nishikawa K, Taketa M, Higuchi K, Tai H, Hirota S, Hojo H, Kawakami T, Hataguchi K, Matsumoto K, Ogata H, Higuchi Y. Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77. Acta Crystallogr F Struct Biol Commun 2022; 78:66-74. [PMID: 35102895 PMCID: PMC8805213 DOI: 10.1107/s2053230x22000188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/05/2022] [Indexed: 02/03/2023] Open
Abstract
Hydrogenases catalyze the reversible oxidation of H2. Carbon monoxide (CO) is known to be a competitive inhibitor of O2-sensitive [NiFe]-hydrogenases. Although the activities of some O2-tolerant [NiFe]-hydrogenases are unaffected by CO, the partially O2-tolerant [NiFe]-hydrogenase from Citrobacter sp. S-77 (S77-HYB) is inhibited by CO. In this work, the CO-bound state of S77-HYB was characterized by activity assays, spectroscopic techniques and X-ray crystallography. Electron paramagnetic resonance spectroscopy showed a diamagnetic Ni2+ state, and Fourier-transform infrared spectroscopy revealed the stretching vibration of the exogenous CO ligand. The crystal structure determined at 1.77 Å resolution revealed that CO binds weakly to the nickel ion in the Ni-Fe active site of S77-HYB. These results suggest a positive correlation between O2 and CO tolerance in [NiFe]-hydrogenases.
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Affiliation(s)
- Takahiro Imanishi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Koji Nishikawa
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Midori Taketa
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Katsuhiro Higuchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hulin Tai
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department of Chemistry, Yanbian University, Yanji 133002, Jilin, People’s Republic of China
| | - Shun Hirota
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Kiriko Hataguchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kayoko Matsumoto
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hideaki Ogata
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
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3
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Tai H, Higuchi Y, Hirota S. Comprehensive reaction mechanisms at and near the Ni-Fe active sites of [NiFe] hydrogenases. Dalton Trans 2018. [PMID: 29532823 DOI: 10.1039/c7dt04910b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
[NiFe] hydrogenase (H2ase) catalyzes the oxidation of dihydrogen to two protons and two electrons and/or its reverse reaction. For this simple reaction, the enzyme has developed a sophisticated but intricate mechanism with heterolytic cleavage of dihydrogen (or a combination of a hydride and a proton), where its Ni-Fe active site exhibits various redox states. Recently, thermodynamic parameters of the acid-base equilibrium for activation-inactivation, a new intermediate in the catalytic reaction, and new crystal structures of [NiFe] H2ases have been reported, providing significant insights into the activation-inactivation and catalytic reaction mechanisms of [NiFe] H2ases. This Perspective provides an overview of the reaction mechanisms of [NiFe] H2ases based on these new findings.
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Affiliation(s)
- Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.
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4
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part II. [4Fe-4S] and [3Fe-4S] iron-sulfur proteins. J Struct Biol 2018; 202:250-263. [DOI: 10.1016/j.jsb.2018.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/11/2018] [Accepted: 01/29/2018] [Indexed: 01/27/2023]
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5
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Breglia R, Greco C, Fantucci P, De Gioia L, Bruschi M. Theoretical investigation of aerobic and anaerobic oxidative inactivation of the [NiFe]-hydrogenase active site. Phys Chem Chem Phys 2018; 20:1693-1706. [DOI: 10.1039/c7cp06228a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H2) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H2 production processes.
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Affiliation(s)
- Raffaella Breglia
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Claudio Greco
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Maurizio Bruschi
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
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6
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Abstract
Hydrogenases are enzymes of great biotechnological relevance because they catalyse the interconversion of H2, water (protons) and electricity using non-precious metal catalytic active sites. Electrochemical studies into the reactivity of NiFe membrane-bound hydrogenases (MBH) have provided a particularly detailed insight into the reactivity and mechanism of this group of enzymes. Significantly, the control centre for enabling O2 tolerance has been revealed as the electron-transfer relay of FeS clusters, rather than the NiFe bimetallic active site. The present review paper will discuss how electrochemistry results have complemented those obtained from structural and spectroscopic studies, to present a complete picture of our current understanding of NiFe MBH.
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7
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Sun P, Yang D, Li Y, Zhang Y, Su L, Wang B, Qu J. Thiolate-Bridged Nickel–Iron and Nickel–Ruthenium Complexes Relevant to the CO-Inhibited State of [NiFe]-Hydrogenase. Organometallics 2016. [DOI: 10.1021/acs.organomet.5b01035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Puhua Sun
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Faculty
of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, 2 Linggong Road, Dalian 116024, People’s Republic of China
| | - Dawei Yang
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Faculty
of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, 2 Linggong Road, Dalian 116024, People’s Republic of China
| | - Ying Li
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Faculty
of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, 2 Linggong Road, Dalian 116024, People’s Republic of China
| | - Yahui Zhang
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Faculty
of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, 2 Linggong Road, Dalian 116024, People’s Republic of China
| | - Linan Su
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Faculty
of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, 2 Linggong Road, Dalian 116024, People’s Republic of China
| | - Baomin Wang
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Faculty
of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, 2 Linggong Road, Dalian 116024, People’s Republic of China
| | - Jingping Qu
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Faculty
of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, 2 Linggong Road, Dalian 116024, People’s Republic of China
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8
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Structural differences of oxidized iron–sulfur and nickel–iron cofactors in O 2 -tolerant and O 2 -sensitive hydrogenases studied by X-ray absorption spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:162-170. [DOI: 10.1016/j.bbabio.2014.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022]
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9
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Volbeda A, Martin L, Barbier E, Gutiérrez-Sanz O, De Lacey AL, Liebgott PP, Dementin S, Rousset M, Fontecilla-Camps JC. Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states. J Biol Inorg Chem 2015; 20:11-22. [PMID: 25315838 DOI: 10.1007/s00775-014-1203-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/01/2014] [Indexed: 01/12/2023]
Abstract
Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.
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Affiliation(s)
- Anne Volbeda
- University Grenoble Alpes, IBS, 38044, Grenoble, France. .,CEA, IBS, 38044, Grenoble, France. .,CNRS, IBS, 38044, Grenoble, France.
| | - Lydie Martin
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France
| | - Elodie Barbier
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France.,CEA, MINATEC, 38044, Grenoble, France
| | | | | | - Pierre-Pol Liebgott
- Aix-Marseille Université, CNRS, IMM, 13402, Marseille, France.,Aix-Marseille Université, CNRS/INSU, MIO, 13288, Marseille, France
| | | | - Marc Rousset
- Aix-Marseille Université, CNRS, IMM, 13402, Marseille, France.,Consulate General of France, 205 N Michigan Ave, Chicago, IL, 60601, USA
| | - Juan C Fontecilla-Camps
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France
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10
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Abstract
An oxygen-tolerant respiratory [NiFe]-hydrogenase is proven to be a four-electron hydrogen/oxygen oxidoreductase, catalyzing the reaction 2 H2 + O2 = 2 H2O, equivalent to hydrogen combustion, over a sustained period without inactivating. At least 86% of the H2O produced by Escherichia coli hydrogenase-1 exposed to a mixture of 90% H2 and 10% O2 is accounted for by a direct four-electron pathway, whereas up to 14% arises from slower side reactions proceeding via superoxide and hydrogen peroxide. The direct pathway is assigned to O2 reduction at the [NiFe] active site, whereas the side reactions are an unavoidable consequence of the presence of low-potential relay centers that release electrons derived from H2 oxidation. The oxidase activity is too slow to be useful in removing O2 from the bacterial periplasm; instead, the four-electron reduction of molecular oxygen to harmless water ensures that the active site survives to catalyze sustained hydrogen oxidation.
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11
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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12
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Engineering Hydrogenases for H2 Production: Bolts and Goals. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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13
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Abou Hamdan A, Burlat B, Gutiérrez-Sanz O, Liebgott PP, Baffert C, De Lacey AL, Rousset M, Guigliarelli B, Léger C, Dementin S. O2-independent formation of the inactive states of NiFe hydrogenase. Nat Chem Biol 2012; 9:15-7. [DOI: 10.1038/nchembio.1110] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 09/27/2012] [Indexed: 11/09/2022]
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14
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Bolligarla R, Das SK. Sulfur Oxygenation of [Ni(btdt)
2
]
2–
by Aerial Oxidation under Ambient Conditions – Syntheses, Crystal Structures, and Properties of [Bu
4
N]
2
[Ni(btdt)
2
] and [Bu
4
N]
2
[Ni(btdtO
2
)
2
]·H
2
O ({btdt}
2–
= 2,1,3‐Benzenethiadiazole‐5,6‐dithiolate). Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201101426] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ramababu Bolligarla
- School of Chemistry, University of Hyderabad, P. O. Central University, Hyderabad 500046, Andhra Pradesh, India, Fax: +91‐40‐2301‐2460
| | - Samar K. Das
- School of Chemistry, University of Hyderabad, P. O. Central University, Hyderabad 500046, Andhra Pradesh, India, Fax: +91‐40‐2301‐2460
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15
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16
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Matsumoto T, Kabe R, Nonaka K, Ando T, Yoon KS, Nakai H, Ogo S. Model study of CO inhibition of [NiFe]hydrogenase. Inorg Chem 2011; 50:8902-6. [PMID: 21853978 DOI: 10.1021/ic200965t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a modified mechanism for the inhibition of [NiFe]hydrogenase ([NiFe]H(2)ase) by CO. We present a model study, using a NiRu H(2)ase mimic, that demonstrates that (i) CO completely inhibits the catalytic cycle of the model compound, (ii) CO prefers to coordinate to the Ru(II) center rather than taking an axial position on the Ni(II) center, and (iii) CO is unable to displace a hydrido ligand from the NiRu center. We combine these studies with a reevaluation of previous studies to propose that, under normal circumstances, CO inhibits [NiFe]H(2)ase by complexing to the Fe(II) center.
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Affiliation(s)
- Takahiro Matsumoto
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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17
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Ohki Y, Tatsumi K. Thiolate‐Bridged Iron–Nickel Models for the Active Site of [NiFe] Hydrogenase. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.201001087] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science, and Research Center for Materials Science, Nagoya University, Furo‐cho, Chikusa‐ku, 464–8602, Nagoya, Japan, Fax: +81‐52‐789‐2943
| | - Kazuyuki Tatsumi
- Department of Chemistry, Graduate School of Science, and Research Center for Materials Science, Nagoya University, Furo‐cho, Chikusa‐ku, 464–8602, Nagoya, Japan, Fax: +81‐52‐789‐2943
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18
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Ogata H, Kellers P, Lubitz W. The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state). J Mol Biol 2010; 402:428-44. [PMID: 20673834 DOI: 10.1016/j.jmb.2010.07.041] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 11/18/2022]
Abstract
The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 Å resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino acid sequence identity is ∼ 50%. The bimetallic [NiFe] active site is located in the large subunit of the heterodimer and possesses three diatomic non-protein ligands coordinated to the Fe (two CN(-) , one CO). Ni is bound to the protein backbone via four cysteine thiolates; two of them also bridge the two metals. One of the bridging cysteines (Cys64) exhibits a modified thiolate in part of the sample. A mono-oxo bridging ligand was assigned between the metal ions of the catalytic center. This is in contrast to a proposal for Desulfovibrio sp. hydrogenases that show a di-oxo species in this position for the Ni-A state. The additional metal site located in the large subunit appears to be a Mg(2+) ion. Three iron-sulfur clusters were found in the small subunit that forms the electron transfer chain connecting the catalytic site with the molecular surface. The calculated anomalous Fourier map indicates a distorted proximal iron-sulfur cluster in part of the crystals. This altered proximal cluster is supposed to be paramagnetic and is exchange coupled to the Ni(3+) ion and the medial [Fe(3)S(4)](+) cluster that are both EPR active (S=1/2 species). This finding of a modified proximal cluster in the [NiFe] hydrogenase might explain the observation of split EPR signals that are occasionally detected in the oxidized state of membrane-bound [NiFe] hydrogenases as from A. vinosum.
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Affiliation(s)
- Hideaki Ogata
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
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19
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Gutiérrez-Sánchez C, Rüdiger O, Fernández VM, De Lacey AL, Marques M, Pereira IAC. Interaction of the active site of the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough with carbon monoxide and oxygen inhibitors. J Biol Inorg Chem 2010; 15:1285-92. [PMID: 20669037 DOI: 10.1007/s00775-010-0686-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 07/06/2010] [Indexed: 11/30/2022]
Abstract
The study of Ni-Fe-Se hydrogenases is interesting from the basic research point of view because their active site is a clear example of how nature regulates the catalytic function of an enzyme by the change of a single residue, in this case a cysteine, which is replaced by a selenocysteine. Most hydrogenases are inhibited by CO and O(2). In this work we studied these inhibition processes for the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough by combining catalytic activity measurements, followed by mass spectrometry or chronoamperometry, with Fourier transform IR spectroscopy experiments. The results show that the CO inhibitor binds to Ni in both conformations of the active site of this hydrogenase in a way similar to that in standard Ni-Fe hydrogenases, although in one of the CO-inhibited conformations the active site of the Ni-Fe-Se hydrogenase is more protected against the attack by O(2). The inhibition of the Ni-Fe-Se hydrogenase activity by O(2) could be explained by oxidation of the terminal cysteine ligand of the active-site Ni, instead of the direct attack of O(2) on the bridging site between Ni and Fe.
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20
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Pandelia ME, Ogata H, Lubitz W. Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site. Chemphyschem 2010; 11:1127-40. [PMID: 20301175 DOI: 10.1002/cphc.200900950] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The [NiFe] hydrogenase from the anaerobic sulphate reducing bacterium Desulfovibrio vulgaris Miyazaki F is an excellent model for constructing a mechanism for the function of the so-called 'oxygen-sensitive' hydrogenases. The present review focuses on spectroscopic investigations of the active site intermediates playing a role in the activation/deactivation and catalytic cycle of this enzyme as well as in the inhibition by carbon monoxide or molecular oxygen and the light-sensitivity of the hydrogenase. The methods employed include magnetic resonance and vibrational (FTIR) techniques combined with electrochemistry that deliver information about details of the geometrical and electronic structure of the intermediates and their redox behaviour. Based on these data a mechanistic scheme is developed.
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Affiliation(s)
- Maria-Eirini Pandelia
- Max-Planck Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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Marques MC, Coelho R, De Lacey AL, Pereira IA, Matias PM. The Three-Dimensional Structure of [NiFeSe] Hydrogenase from Desulfovibrio vulgaris Hildenborough: A Hydrogenase without a Bridging Ligand in the Active Site in Its Oxidised, “as-Isolated” State. J Mol Biol 2010; 396:893-907. [DOI: 10.1016/j.jmb.2009.12.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 12/03/2009] [Accepted: 12/10/2009] [Indexed: 10/20/2022]
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Schwarz C, Poss Z, Hoffmann D, Appel J. Hydrogenases and Hydrogen Metabolism in Photosynthetic Prokaryotes. RECENT ADVANCES IN PHOTOTROPHIC PROKARYOTES 2010; 675:305-48. [DOI: 10.1007/978-1-4419-1528-3_18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Liu T, Li B, Singleton ML, Hall MB, Darensbourg MY. Sulfur oxygenates of biomimetics of the diiron subsite of the [FeFe]-hydrogenase active site: properties and oxygen damage repair possibilities. J Am Chem Soc 2009; 131:8296-307. [PMID: 19507910 DOI: 10.1021/ja9016528] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study explores the site specificity (sulfur vs the Fe-Fe bond) of oxygenation of diiron (Fe(I)Fe(I) and Fe(II)Fe(II)) organometallics that model the 2-iron subsite in the active site of [FeFe]-hydrogenase: (mu-pdt)[Fe(CO)(2)L][Fe(CO)(2)L'] (L = L' = CO (1); L = PPh(3), L' = CO (2); L = L' = PMe(3) (4)) and (mu-pdt)(mu-H)[Fe(CO)(2)PMe(3)](2) (5). DFT computations find that the Fe-Fe bond in the Fe(I)Fe(I) diiron models is thermodynamically favored to produce the mu-oxo or oxidative addition product, Fe(II)-O-Fe(II); nevertheless, the sulfur-based HOMO-1 accounts for the experimentally observed mono- and bis-O-atom adducts at sulfur, i.e., (mu-pst)[Fe(CO)(2)L][Fe(CO)(2)L'] (pst = -S(CH(2))(3)S(O)-, 1,3-propanesulfenatothiolate; L = L' = CO (1-O); L = PPh(3), L' = CO (2-O); L = L' = PMe(3) (4-O)) and (mu-pds)[Fe(CO)(2)L][Fe(CO)(2)L'] (pds = -(O)S(CH(2))(3)S(O)-, 1,3-propanedisulfenato; L = PPh(3), L' = CO (2-O(2))). The Fe(II)(mu-H)Fe(II) diiron model (5), for which the HOMO is largely of sulfur character, exclusively yields S-oxygenation. The depressing effect of such bridging ligand modification on the dynamic NMR properties arising from rotation of the Fe(CO)(3) correlates with higher barriers to the CO/PMe(3) exchange of (mu-pst)[Fe(CO)(3)](2) as compared to (mu-pdt)[Fe(CO)(3)](2). Five molecular structures are confirmed by X-ray diffraction: 1-O, 2-O, 2-O(2), 4-O, and 6. Deoxygenation with reclamation of the mu-pdt parent complex occurs in a proton/electron-coupled process. The possible biological relevance of oxygenation and deoxygenation studies is discussed.
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Affiliation(s)
- Tianbiao Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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Peters JW. Carbon Monoxide and Cyanide Ligands in the Active Site of [FeFe]-Hydrogenases. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The [FeFe]-hydrogenases, although share common features when compared to other metal containing hydrogenases, clearly have independent evolutionary origins. Examples of [FeFe]-hydrogenases have been characterized in detail by biochemical and spectroscopic approaches and the high resolution structures of two examples have been determined. The active site H-cluster is a complex bridged metal assembly in which a [4Fe-4S] cubane is bridged to a 2Fe subcluster with unique non-protein ligands including carbon monoxide, cyanide, and a five carbon dithiolate. Carbon monoxide and cyanide ligands as a component of a native active metal center is a property unique to the metal containing hydrogenases and there has been considerable attention to the characterization of the H-cluster at the level of electronic structure and mechanism as well as to defining the biological means to synthesize such a unique metal cluster. The chapter describes the structural architecture of [FeFe]-hydrogenases and key spectroscopic observations that have afforded the field with a fundamental basis for understanding the relationship between structure and reactivity of the H-cluster. In addition, the results and ideas concerning the topic of H-cluster biosynthesis as an emerging and fascinating area of research, effectively reinforcing the potential linkage between iron-sulfur biochemistry to the role of iron-sulfur minerals in prebiotic chemistry and the origin of life.
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Affiliation(s)
- John W. Peters
- Montana State University, Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center Bozeman, MT 59717 USA
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Fontecilla-Camps JC. Structure and Function of [NiFe]-Hydrogenases. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
[NiFe(Se)]-hydrogenases are hetero-dimeric enzymes present in many microorganisms where they catalyze the oxidation of molecular hydrogen or the reduction of protons. Like the other two types of hydrogen-metabolizing enzymes, the [FeFe]- and [Fe]-hydrogenases, [NiFe]-hydrogenases have a Fe(CO)x unit in their active sites that is most likely involved in hydride binding. Because of their complexity, hydrogenases require a maturation machinery that involves several gene products. They include nickel and iron transport, synthesis of CN− (and maybe CO), formation and insertion of a FeCO(CN−)2 unit in the apo form, insertion of nickel and proteolytic cleavage of a C-terminal stretch, a step that ends the maturation process. Because the active site is buried in the structure, electron and proton transfer are required between this site and the molecular surface. The former is mediated by either three or one Fe/S cluster(s) depending on the enzyme. When exposed to oxidizing conditions, such as the presence of O2, [NiFe]-hydrogenases are inactivated. Depending on the redox state of the enzyme, exposure to oxygen results in either a partially reduced oxo species probably a (hydro)peroxo ligand between nickel and iron or a more reduced OH– ligand instead. Under some conditions the thiolates that coordinate the NiFe center can be modified to sulfenates. Understanding this process is of biotechnological interest for H2 production by photosynthetic organisms.
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Affiliation(s)
- Juan C. Fontecilla-Camps
- Laboratoire de Cristallographie et de Cristallogenèse des Proteines, Institut de Biologie Structurale J. P. Ebel (CEA-CNRS-UJF) 41 rue Jules Horowitz F-38027 Grenoble Cédex 1 France
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Rakowski DuBois M, DuBois DL. The roles of the first and second coordination spheres in the design of molecular catalysts for H2production and oxidation. Chem Soc Rev 2009; 38:62-72. [DOI: 10.1039/b801197b] [Citation(s) in RCA: 548] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ogata H, Lubitz W, Higuchi Y. [NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism. Dalton Trans 2009:7577-87. [DOI: 10.1039/b903840j] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nickel–thiolate and iron–thiolate cyanocarbonyl complexes: Modeling the nickel and iron sites of [NiFe] hydrogenase. CR CHIM 2008. [DOI: 10.1016/j.crci.2008.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y. Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem Rev 2007; 107:4273-303. [PMID: 17850165 DOI: 10.1021/cr050195z] [Citation(s) in RCA: 1004] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Juan C Fontecilla-Camps
- Laboratoire de Cristallographie et Cristallogenèse des Proteines, Institut de Biologie Structurale J. P. Ebel, CEA, CNRS, Universitè Joseph Fourier, 41 rue J. Horowitz, 38027 Grenoble Cedex 1, France.
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Vincent KA, Parkin A, Armstrong FA. Investigating and Exploiting the Electrocatalytic Properties of Hydrogenases. Chem Rev 2007; 107:4366-413. [PMID: 17845060 DOI: 10.1021/cr050191u] [Citation(s) in RCA: 554] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kylie A Vincent
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
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33
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Lubitz W, Reijerse E, van Gastel M. [NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques. Chem Rev 2007; 107:4331-65. [PMID: 17845059 DOI: 10.1021/cr050186q] [Citation(s) in RCA: 376] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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De Lacey AL, Fernandez VM, Rousset M, Cammack R. Activation and Inactivation of Hydrogenase Function and the Catalytic Cycle: Spectroelectrochemical Studies. Chem Rev 2007; 107:4304-30. [PMID: 17715982 DOI: 10.1021/cr0501947] [Citation(s) in RCA: 364] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio L De Lacey
- Instituto de CatAlisis, CSIC, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
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35
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Agrawal AG, Voordouw G, Gärtner W. Sequential and structural analysis of [NiFe]-hydrogenase-maturation proteins from Desulfovibrio vulgaris Miyazaki F. Antonie van Leeuwenhoek 2006; 90:281-90. [PMID: 16902753 DOI: 10.1007/s10482-006-9082-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 05/02/2006] [Indexed: 11/25/2022]
Abstract
The complete primary structure of the hyn-region in the genome of Desulfovibrio vulgaris Miyazaki F (DvMF), encoding the [NiFe]-hydrogenase and two maturation proteins has been identified. Besides the formerly reported genes for the large and small subunits, this region comprises genes encoding an endopeptidase (HynC) and a putative chaperone (HynD). The complete genomic region covers 4086 nucleotides including the previously published upstream located promoter region and the sequences of the structural genes. A phylogenetic tree for both maturation proteins shows strongest sequential relationship to the orthologous proteins of Desulfovibrio vulgaris Hildenborough (DvH). Secondary structure prediction for HynC (168 aa, corresponding to a molecular weight of 17.9 kDa) revealed a practically identical arrangement of alpha-helical and beta-strand elements between the orthologous protein HybD from E. coli and allowed a three-dimensional modelling of HynC on the basis of the formerly published structure of HybD. The putative chaperone HynD consists of 83 aa (molecular weight of 9 kDa) and shows 76% homology to DvH HynD. Preliminary experiments demonstrate that the operon is expressed under the control of its own promoter in Escherichia coli, although no further processing could be observed, providing evidence that additional proteins have to be involved in the maturation process. Accession numbers: DQ072852, HynC protein ID AAY90127, HynD protein ID AAY90128.
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Affiliation(s)
- Aruna Goenka Agrawal
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstr. 34-36, 45470, Mülheim, Germany
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37
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Vincent KA, Belsey NA, Lubitz W, Armstrong FA. Rapid and Reversible Reactions of [NiFe]-Hydrogenases with Sulfide. J Am Chem Soc 2006; 128:7448-9. [PMID: 16756292 DOI: 10.1021/ja061732f] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid and reversible binding of sulfide to [NiFe]-hydrogenases (particularly the enzyme from Desulfovibrio vulgaris) under weakly acidic conditions (pH 6) has been studied by protein film voltammetry, which tracks the formation of different species as a function of potential. Sulfide (most likely entering as H2S) rapidly attacks the active site during H2 oxidation. The inactive adduct is formed (and is stable) only at potentials substantially more positive than the comparable species formed with oxygen species and is easily reactivated upon reduction. The sulfide adduct also reacts further with O2 to produce a new species that undergoes reductive activation very slowly. The results clarify complex and controversial chemistry reported in the literature and provide insight into how these enzymes would cope with sulfide production in sulfate-reducing bacteria.
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Affiliation(s)
- Kylie A Vincent
- Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
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38
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Chen CH, Lee GH, Liaw WF. Mononuclear [NiII(L)(P-(o-C6H4S)2(o-C6H4SH))]0/1- (L = Thiolate, Selenolate, PPh3, and Cl) Complexes with Intramolecular [Ni···S···H···S]/[Ni···H···S] Interactions Modulated by the Coordinated Ligand L: Relevance to the [NiFe] Hydrogenases. Inorg Chem 2006; 45:2307-16. [PMID: 16499397 DOI: 10.1021/ic051924w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The shift of the IR nu(S)(-)(H) frequency to lower wavenumbers for the series of complexes [Ni(II)(L)(P-(o-C6H4S)2(o-C6H4SH))]0/1- (L = PPh3 (1), Cl (6), Se-p-C6H4-Cl (5), S-C4H3S (7), SePh (4)) indicates that a trend of increasing electronic donation of the L ligands coordinated to the Ni(II) center promotes intramolecular [Ni-S...H-S] interactions. Compared to the Ni...S(H) distance, in the range of 3.609-3.802 A in complexes 1 and 4-7, the Ni...S(CH3) distances of 2.540 and 2.914 A observed in the [Ni(II)(PPh3)(P(o-C6H4S)2(o-C6H4-SCH3))] complexes (8a and 8b, two conformational isomers with the chemical shift of the thioether methyl group at delta 1.820 (-60 degrees C) and 2.109 ppm (60 degrees C) (C4D8O)) and the Ni...S(CH3) distances of 3.258 and 3.229 A found in the [Ni(II)(L)(P(o-C6H4S)2(o-C6H4-SCH3))]1- complexes (L = SPh (9), SePh (10)) also support the idea that the pendant thiol protons of the Ni(II)-thiol complexes 1/4-7 were attracted by both the sulfur of thiolate and the nickel. The increased basicity (electronic density) of the nickel center regulated by the monodentate ligand attracted the proton of the pendant thiol effectively and caused the weaker S...H bond. In addition, the pendant thiol interaction modes in the solid state (complexes 1a and 1b, Scheme 1) may be controlled by the solvent of crystallization. Compared to complex 1a, the stronger intramolecular [Ni-S...H-S] interaction (or a combination of [Ni-S...H-S]/[Ni...H-S] interactions) found in complexes 4-7 led to the weaker S-H bond strength and accelerated the oxidation (by O2) of complexes 4-7 to produce the [Ni(Y)(L)(P(o-C6H4S)3)]1- (L = Se-p-C6H4-Cl (11), SePh (12), S-C4H3S (13)) complexes.
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Affiliation(s)
- Chien-Hong Chen
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan
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39
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van der Linden E, Burgdorf T, de Lacey AL, Buhrke T, Scholte M, Fernandez VM, Friedrich B, Albracht SPJ. An improved purification procedure for the soluble [NiFe]-hydrogenase of Ralstonia eutropha: new insights into its (in)stability and spectroscopic properties. J Biol Inorg Chem 2006; 11:247-60. [PMID: 16418856 DOI: 10.1007/s00775-005-0075-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Accepted: 12/12/2005] [Indexed: 11/28/2022]
Abstract
Infrared (IR) spectra in combination with chemical analyses have recently shown that the active Ni-Fe site of the soluble NAD(+)-reducing [NiFe]-hydrogenase from Ralstonia eutropha contains four cyanide groups and one carbon monoxide as ligands. Experiments presented here confirm this result, but show that a variable percentage of enzyme molecules loses one or two of the cyanide ligands from the active site during routine purification. For this reason the redox conditions during the purification have been optimized yielding hexameric enzyme preparations (HoxFUYHI(2)) with aerobic specific H(2)-NAD(+) activities of 150-185 mumol/min/mg of protein (up to 200% of the highest activity previously reported in the literature). The preparations were highly homogeneous in terms of the active site composition and showed superior IR spectra. IR spectro-electrochemical studies were consistent with the hypothesis that only reoxidation of the reduced enzyme with dioxygen leads to the inactive state, where it is believed that a peroxide group is bound to nickel. Electron paramagnetic resonance experiments showed that the radical signal from the NADH-reduced enzyme derives from the semiquinone form of the flavin (FMN-a) in the hydrogenase module (HoxYH dimer), but not of the flavin (FMN-b) in the NADH-dehydrogenase module (HoxFU dimer). It is further demonstrated that the hexameric enzyme remains active in the presence of NADPH and air, whereas NADH and air lead to rapid destruction of enzyme activity. It is proposed that the presence of NADPH in cells keeps the enzyme in the active state.
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Affiliation(s)
- Eddy van der Linden
- Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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40
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van Gastel M, Stein M, Brecht M, Schröder O, Lendzian F, Bittl R, Ogata H, Higuchi Y, Lubitz W. A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. J Biol Inorg Chem 2005; 11:41-51. [PMID: 16292669 DOI: 10.1007/s00775-005-0048-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Accepted: 10/05/2005] [Indexed: 10/25/2022]
Abstract
The catalytic center of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in the oxidized states was investigated by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy applied to single crystals of the enzyme. The experimental results were compared with density functional theory (DFT) calculations. For the Ni-B state, three hyperfine tensors could be determined. Two tensors have large isotropic hyperfine coupling constants and are assigned to the beta-CH2 protons of the Cys-549 that provides one of the bridging sulfur ligands between Ni and Fe in the active center. From a comparison of the orientation of the third hyperfine tensor with the tensor obtained from DFT calculations an OH- bridging ligand has been identified in the Ni-B state. For the Ni-A state broader signals were observed. The signals of the third proton, as observed for the "ready" state Ni-B, were not observed at the same spectral position for Ni-A, confirming a structural difference involving the bridging ligand in the "unready" state of the enzyme.
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Affiliation(s)
- Maurice van Gastel
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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Ogata H, Hirota S, Nakahara A, Komori H, Shibata N, Kato T, Kano K, Higuchi Y. Activation Process of [NiFe] Hydrogenase Elucidated by High-Resolution X-Ray Analyses: Conversion of the Ready to the Unready State. Structure 2005; 13:1635-42. [PMID: 16271886 DOI: 10.1016/j.str.2005.07.018] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Revised: 07/22/2005] [Accepted: 07/23/2005] [Indexed: 11/24/2022]
Abstract
Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready). We have succeeded in converting Ni-B to Ni-A with the use of Na2S and O2 and determining the high-resolution crystal structures of both states. Ni-B possesses a monatomic nonprotein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species. The terminal atom of the bridging species of Ni-A occupies a similar position as C of the exogenous CO in the CO complex (inhibited state). The common features of the enzyme structures at the unready (Ni-A) and inhibited (CO complex) states are proposed. These findings provide useful information on the design of new systems of biomimetic dihydrogen production and fuel cell devices.
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Affiliation(s)
- Hideaki Ogata
- Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Ako-gun, Hyogo 678-1297, Japan
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42
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Li Z, Ohki Y, Tatsumi K. Dithiolato-Bridged Dinuclear Iron−Nickel Complexes [Fe(CO)2(CN)2(μ-SCH2CH2CH2S)Ni(S2CNR2)]-Modeling the Active Site of [NiFe] Hydrogenase. J Am Chem Soc 2005; 127:8950-1. [PMID: 15969562 DOI: 10.1021/ja051590+] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[NiFe] hydrogenase, the enzyme of which catalyzes the reversible oxidation of molecular hydrogen to protons and electrons, contains a unique heterodinuclear thiolate-bridged Ni-Fe complex in which the iron center is coordinated by CO and CN. We have synthesized dithiolate-bridged Ni-Fe complexes bearing CO and CN ligands to model the active center of [NiFe] hydrogenase. The Ni-Fe complexes containing a [(CN)2(CO)2Fe(mu-S2)NiS2] framework are the closest yet structural models of [NiFe] hydrogenase.
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Affiliation(s)
- Zilong Li
- Research Center for Materials Science and Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Minnan L, Jinli H, Xiaobin W, Huijuan X, Jinzao C, Chuannan L, Fengzhang Z, Liangshu X. Isolation and characterization of a high H2-producing strain Klebsiella oxytoca HP1 from a hot spring. Res Microbiol 2005; 156:76-81. [PMID: 15636750 DOI: 10.1016/j.resmic.2004.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2004] [Accepted: 08/02/2004] [Indexed: 10/26/2022]
Abstract
A hydrogen-producing bacterial strain was newly isolated from a hot spring and identified as Klebsiella oxytoca HP1 by 16S rRNA gene sequence analysis and detection by BioMerieux Vitek. Important parameters, including substrates, starting pH of culture, temperature and oxygen concentration for batch ferment hydrogen production, were investigated. Among different sugars, glucose and sucrose were the preferred substrates for hydrogen production. The optimal starting pH of culture was about 7.0. The activity was drastically reduced in a prolonged fermentation due to the accumulation of organic acids. Increasing temperatures (from 25 to 35 degrees C) improved the hydrogen production activity. K. oxytoca HP1 produced hydrogen under different concentrations (1-10%) of oxygen in the gas phase, indicating that it is highly resistant to oxygen inhibition. Under batch ferment conditions, the maximal hydrogen production activity, rate and yield were obtained as 9.6 mmol/g dw h, 87.5 ml/l h and 1.0 mol/mol glucose (conversion 16.7%), respectively. In continuous hydrogen production, the maximum activity, rate and yield were 15.2 mmol/g dw h, 350.0 ml/l h and 3.6 mol/mol sucrose (conversion 32.5%), respectively. These results indicate that K. oxytoca HP1 is an ideal hydrogen producer.
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Affiliation(s)
- L Minnan
- Key Laboratory of the Ministry of Education for Cell Biology and Tumor Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, PR China.
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44
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Armstrong FA, Albracht SPJ. [NiFe]-hydrogenases: spectroscopic and electrochemical definition of reactions and intermediates. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:937-54; discussion 1035-40. [PMID: 15991402 DOI: 10.1098/rsta.2004.1528] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Production and usage of di-hydrogen, H2, in micro-organisms is catalysed by highly active, 'ancient' metalloenzymes known as hydrogenases. Based on the number and identity of metal atoms in their active sites, hydrogenases fall into three main classes, [NiFe]-, [FeFe]- and [Fe]-. All contain the unusual ligand CO (and in most cases CN- as well) making them intriguing examples of 'organometallic' cofactors. These ligands render the active sites superbly 'visible' using infrared spectroscopy, which complements the use of electron paramagnetic resonance spectroscopy in studying mechanisms and identifying intermediates. Hydrogenases are becoming a focus of attention for research into future energy technologies, not only H2 production but also H2 oxidation in fuel cells. Hydrogenases immobilized on electrodes exhibit high electrocatalytic activity, providing not only an important new technique for their investigation, but also a basis for novel fuel cells either using the enzyme itself, or inspired synthetic catalysts. Favourable comparisons have been made with platinum electrocatalysts, an advantage of enzymes being their specificity for H2 and tolerance of CO. A challenge for exploiting hydrogenases is their sensitivity to O2, but some organisms are known to produce enzymes that overcome this problem by subtle alterations of the active site and gas access channels.
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Affiliation(s)
- Fraser A Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, UK.
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Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SPJ, Garcin E, Rousset M, Fontecilla-Camps JC. Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases. J Biol Inorg Chem 2005; 10:239-49. [PMID: 15803334 DOI: 10.1007/s00775-005-0632-x] [Citation(s) in RCA: 278] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 02/02/2005] [Indexed: 11/29/2022]
Abstract
[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.
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Affiliation(s)
- Anne Volbeda
- Laboratoire de Cristallographie et de Cristallogenèse des Protèines, Institut de Biologie Structurale J.P. Ebel (CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027, Grenoble Cédex 1, France.
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Stein M, Lubitz W. Relativistic DFT calculation of the reaction cycle intermediates of [NiFe] hydrogenase: a contribution to understanding the enzymatic mechanism. J Inorg Biochem 2005; 98:862-77. [PMID: 15134933 DOI: 10.1016/j.jinorgbio.2004.03.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2003] [Revised: 03/18/2004] [Accepted: 03/22/2004] [Indexed: 10/26/2022]
Abstract
Structures and spectroscopic observables of the paramagnetic intermediates of the enzymatic reaction cycle of the metalloenzyme [NiFe] hydrogenase were calculated using relativistic density functional theory (DFT) within the zero-order regular approximation (ZORA). By comparing experimental and calculated magnetic resonance parameters (g- and hyperfine tensors) for the states Ni-A, Ni-B, Ni-C, Ni-L, and Ni-CO the details of the atomic composition of these paramagnetic intermediates could be elucidated that are mostly not available from X-ray structure analysis. In general, good agreement between calculated and experimental observables could be obtained. A detailed picture of the changes of the active center during the catalytic cycle was deduced from the obtained structures. Based on these results, a consistent model for the sequence of redox states including protonation steps is proposed which is important for understanding the mechanism of the [NiFe] hydrogenase.
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Affiliation(s)
- Matthias Stein
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
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Foerster S, van Gastel M, Brecht M, Lubitz W. An orientation-selected ENDOR and HYSCORE study of the Ni-C active state of Desulfovibrio vulgaris Miyazaki F hydrogenase. J Biol Inorg Chem 2004; 10:51-62. [PMID: 15611882 DOI: 10.1007/s00775-004-0613-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Accepted: 11/09/2004] [Indexed: 11/26/2022]
Abstract
Electron nuclear double resonance (ENDOR) and hyperfine sublevel correlation spectroscopy (HYSCORE) are applied to study the active site of catalytic [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F in the reduced Ni-C state. These techniques offer a powerful tool for detecting nearby magnetic nuclei, including a metal-bound substrate hydrogen, and for mapping the spin density distribution of the unpaired electron at the active site. The observed hyperfine couplings are assigned via comparison with structural data from X-ray crystallography and knowledge of the complete g-tensor in the Ni-C state (Foerster et al. (2003) J Am Chem Soc 125:83-93). This is found to be in good agreement with density functional theory calculations. The two most strongly coupled protons (a(iso)=13.7, 11.8 MHz) are assigned to the beta-CH(2) protons of the nickel-coordinating cysteine 549, and a third proton (a(iso)=8.9 MHz) is assigned to a beta-CH(2) proton of cysteine 546. Using D(2)O exchange experiments, the presence of a hydride in the bridging position between the nickel and iron-recently been detected for a regulatory hydrogenase (Brecht et al. (2003) J Am Chem Soc 125:13075-13083)-is experimentally confirmed for the first time for catalytic hydrogenases. The hydride exhibits a small isotropic hyperfine coupling constant (a(iso)=-3.5 MHz) since it is bound to Ni in a direction perpendicular to the z-axis of the Ni (3d(z)(2)) orbital. Nitrogen signals that belong to the nitrogen N(epsilon) of His-88 have been identified. This residue forms a hydrogen bond with the spin-carrying Ni-coordinated sulfur of Cys-549. Comparison with other hydrogenases reveals that the active site is essentially the same in all proteins, including a regulatory hydrogenase.
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Affiliation(s)
- Stefanie Foerster
- Max-Planck-Institut für Bioanorganische Chemie, P.O. Box 10 13 65, 45413 Mülheim an der Ruhr, Germany
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Kurkin S, George SJ, Thorneley RNF, Albracht SPJ. Hydrogen-induced activation of the [NiFe]-hydrogenase from Allochromatium vinosum as studied by stopped-flow infrared spectroscopy. Biochemistry 2004; 43:6820-31. [PMID: 15157116 DOI: 10.1021/bi049854c] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction between hydrogen and the [NiFe]-hydrogenase from Allochromatium vinosum in its inactive form has been studied by stopped-flow infrared spectroscopy. The data, for the first time, clearly show that at room temperature enzyme in the unready state, either oxidized or reduced, does not react with hydrogen. Enzyme in the ready state reacts with hydrogen after a lag phase of about six seconds, whereby a specific reduction of the enzyme occurs. The lag phase and the rate of reduction of the ready enzyme are neither dependent on the enzyme concentration nor on the substrate concentration, i.e., substoichiometric and 8-fold excess amounts of H(2) reduce the ready enzyme at the same rate. Oxygen delays this reaction but does not prevent it. The infrared changes lead us to suggest that the hydroxyl group, bridging between the Ni and the Fe atom in the active site, becomes protonated during this reduction. At physiological temperatures, this property of the inactive ready enzyme enables a full development of activity by substoichiometric H(2) concentrations.
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Affiliation(s)
- Sergei Kurkin
- Swammerdam Institute for Life Sciences, Biochemistry, University of Amsterdam, Plantage Muidergracht 12, NL-1018 TV Amsterdam, The Netherlands
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George SJ, Kurkin S, Thorneley RNF, Albracht SPJ. Reactions of H2, CO, and O2 with active [NiFe]-hydrogenase from Allochromatium vinosum. A stopped-flow infrared study. Biochemistry 2004; 43:6808-19. [PMID: 15157115 DOI: 10.1021/bi049853k] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Ni-Fe site in the active membrane-bound [NiFe]-hydrogenase from Allochromatium vinosum can exist in three different redox states. In the most oxidized state (Ni(a)-S) the nickel is divalent. The most reduced state (Ni(a)-SR) likewise has Ni(2+), while the intermediate state (Ni(a)-C) has Ni(3+). The transitions between these states have been studied by stopped-flow Fourier transform infrared spectroscopy. It is inferred from the data that the Ni(a)-S --> Ni(a)-C* and Ni(a)-C* --> Ni(a)-SR transitions induced by dihydrogen require one of the [4Fe-4S] clusters to be oxidized. Enzyme in the Ni(a)-S* state with all of the iron-sulfur clusters reduced reacts with dihydrogen to form the Ni(a)-SR state in milliseconds. By contrast, when one of the cubane clusters is oxidized, the Ni(a)-S state reacts with dihydrogen to form the Ni(a)-C state with all of the iron-sulfur clusters reduced. The competition between dihydrogen and carbon monoxide for binding to the active site was dependent on the redox state of the nickel ion. Formation of the Ni(a)-S.CO state (Ni(2+)) by reacting CO with enzyme in the Ni(a)-SR and Ni(a)-S states (Ni(2+)) is considerably faster than its formation from enzyme in the Ni(a)-C* (Ni(3+)) state. Excess oxygen converted hydrogen-reduced enzyme to the inactive Ni(r)* state within 158 ms, suggesting a direct reaction at the Ni-Fe site. With lower O(2) concentrations the formation of intermediate states was observed. The results are discussed in the light of the present knowledge of the structure and mechanism of action of the A. vinosum enzyme.
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Affiliation(s)
- Simon J George
- Swammerdam Institute for Life Sciences, Biochemistry, University of Amsterdam, Plantage Muidergracht 12, NL-1018 TV Amsterdam, The Netherlands
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