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El‐khateeb M, Abul‐Futouh H, Alshurafa H, Görls H, Weigand W. Influence of bidentate phosphine ligands on the chemistry of [FeFe]‐hydrogenase model: insight into molecular structures and electrochemical characteristics. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Mohammad El‐khateeb
- Chemistry Department Jordan University of Science and Technology Irbid 22110 Jordan
| | - Hassan Abul‐Futouh
- Department of Pharmacy Al‐Zaytoonah University of Jordan P.O. Box 130 Amman 11733 Jordan
| | - Hadil Alshurafa
- Chemistry Department Jordan University of Science and Technology Irbid 22110 Jordan
| | - Helmar Görls
- Institut für Anorganische und Analytische Chemie Friedrich‐Schiller‐Universität Jena Humbodt‐Straße 2 Jena 07743 Germany
| | - Wolfgang Weigand
- Institut für Anorganische und Analytische Chemie Friedrich‐Schiller‐Universität Jena Humbodt‐Straße 2 Jena 07743 Germany
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2
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Artz JH, Mulder DW, Ratzloff MW, Lubner CE, Zadvornyy OA, LeVan AX, Williams SG, Adams MWW, Jones AK, King PW, Peters JW. Reduction Potentials of [FeFe]-Hydrogenase Accessory Iron-Sulfur Clusters Provide Insights into the Energetics of Proton Reduction Catalysis. J Am Chem Soc 2017. [PMID: 28635269 DOI: 10.1021/jacs.7b02099] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An [FeFe]-hydrogenase from Clostridium pasteurianum, CpI, is a model system for biological H2 activation. In addition to the catalytic H-cluster, CpI contains four accessory iron-sulfur [FeS] clusters in a branched series that transfer electrons to and from the active site. In this work, potentiometric titrations have been employed in combination with electron paramagnetic resonance (EPR) spectroscopy at defined electrochemical potentials to gain insights into the role of the accessory clusters in catalysis. EPR spectra collected over a range of potentials were deconvoluted into individual components attributable to the accessory [FeS] clusters and the active site H-cluster, and reduction potentials for each cluster were determined. The data suggest a large degree of magnetic coupling between the clusters. The distal [4Fe-4S] cluster is shown to have a lower reduction potential (∼ < -450 mV) than the other clusters, and molecular docking experiments indicate that the physiological electron donor, ferredoxin (Fd), most favorably interacts with this cluster. The low reduction potential of the distal [4Fe-4S] cluster thermodynamically restricts the Fdox/Fdred ratio at which CpI can operate, consistent with the role of CpI in recycling Fdred that accumulates during fermentation. Subsequent electron transfer through the additional accessory [FeS] clusters to the H-cluster is thermodynamically favorable.
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Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University , 258 Clark Hall, Pullman, Washington 99163, United States
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Michael W Ratzloff
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University , 258 Clark Hall, Pullman, Washington 99163, United States
| | - Axl X LeVan
- Department of Chemistry and Biochemistry, Montana State University , 224 Chemistry and Biochemistry Building, Bozeman, Montana 59717, United States
| | - S Garrett Williams
- School of Molecular Sciences, Arizona State University , P.O. Box 871604, Tempe, Arizona 85287, United States
| | - Michael W W Adams
- B216B Life Sciences Complex, Department of Biochemistry, The University of Georgia , Athens, Georgia 30602, United States
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University , P.O. Box 871604, Tempe, Arizona 85287, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University , 258 Clark Hall, Pullman, Washington 99163, United States
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3
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Chernev P, Lambertz C, Brünje A, Leidel N, Sigfridsson KGV, Kositzki R, Hsieh CH, Yao S, Schiwon R, Driess M, Limberg C, Happe T, Haumann M. Hydride Binding to the Active Site of [FeFe]-Hydrogenase. Inorg Chem 2014; 53:12164-77. [DOI: 10.1021/ic502047q] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Petko Chernev
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | - Camilla Lambertz
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Annika Brünje
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Nils Leidel
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | | | - Ramona Kositzki
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | - Chung-Hung Hsieh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shenglai Yao
- Department of Chemistry, Technical University Berlin, 10623 Berlin, Germany
| | - Rafael Schiwon
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
| | - Matthias Driess
- Department of Chemistry, Technical University Berlin, 10623 Berlin, Germany
| | - Christian Limberg
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
| | - Thomas Happe
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Michael Haumann
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
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4
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Mulder DW, Ratzloff MW, Shepard EM, Byer AS, Noone SM, Peters JW, Broderick JB, King PW. EPR and FTIR Analysis of the Mechanism of H2 Activation by [FeFe]-Hydrogenase HydA1 from Chlamydomonas reinhardtii. J Am Chem Soc 2013; 135:6921-9. [DOI: 10.1021/ja4000257] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David W. Mulder
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Michael W. Ratzloff
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Eric M. Shepard
- Department
of Chemistry and
Biochemistry, Montana State University,
Bozeman, Montana 59717, United States
| | - Amanda S. Byer
- Department
of Chemistry and
Biochemistry, Montana State University,
Bozeman, Montana 59717, United States
| | - Seth M. Noone
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - John W. Peters
- Department
of Chemistry and
Biochemistry, Montana State University,
Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Department
of Chemistry and
Biochemistry, Montana State University,
Bozeman, Montana 59717, United States
| | - Paul W. King
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
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5
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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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6
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Harb MK, Niksch T, Windhager J, Görls H, Holze R, Lockett LT, Okumura N, Evans DH, Glass RS, Lichtenberger DL, El-khateeb M, Weigand W. Synthesis and Characterization of Diiron Diselenolato Complexes Including Iron Hydrogenase Models. Organometallics 2009. [DOI: 10.1021/om800748p] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mohammad K. Harb
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Tobias Niksch
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Jochen Windhager
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Helmar Görls
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Rudolf Holze
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - L. Tori Lockett
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Noriko Okumura
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Dennis H. Evans
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Richard S. Glass
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Dennis L. Lichtenberger
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Mohammad El-khateeb
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
| | - Wolfgang Weigand
- Institut für Anorganische and Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Strasse 2, 07743 Jena, Germany, Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan, Institut für Chemie, Technische Universität Chemnitz, Strasse der Nationen 62, 09111 Chemnitz, Germany, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721
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7
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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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8
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Roseboom W, De Lacey AL, Fernandez VM, Hatchikian EC, Albracht SPJ. The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. II. Redox properties, light sensitivity and CO-ligand exchange as observed by infrared spectroscopy. J Biol Inorg Chem 2005; 11:102-18. [PMID: 16323019 DOI: 10.1007/s00775-005-0040-2] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 09/26/2005] [Indexed: 10/25/2022]
Abstract
In [FeFe]-hydrogenases, the H cluster (hydrogen-activating cluster) contains a di-iron centre ([2Fe]H subcluster, a (L)(CO)(CN)Fe(mu-RS2)(mu-CO)Fe(CysS)(CO)(CN) group) covalently attached to a cubane iron-sulphur cluster ([4Fe-4S]H subcluster). The Cys-thiol functions as the link between one iron (called Fe1) of the [2Fe]H subcluster and one iron of the cubane subcluster. The other iron in the [2Fe]H subcluster is called Fe2. The light sensitivity of the Desulfovibrio desulfuricans enzyme in a variety of states has been studied with infrared (IR) spectroscopy. The aerobic inactive enzyme (H(inact) state) and the CO-inhibited active form (H(ox)-CO state) were stable in light. Illumination of the H(ox) state led to a kind of cannibalization; in some enzyme molecules the H cluster was destroyed and the released CO was captured by the H clusters in other molecules to form the light-stable H(ox)-CO state. Illumination of active enzyme under 13CO resulted in the complete exchange of the two intrinsic COs bound to Fe2. At cryogenic temperatures, light induced the photodissociation of the extrinsic CO and the bridging CO of the enzyme in the H(ox)-CO state. Electrochemical redox titrations showed that the enzyme in the H(inact) state converts to the transition state (H(trans)) in a reversible one-electron redox step (E (m, pH 7) = -75 mV). IR spectra demonstrate that the added redox equivalent not only affects the [4Fe-4S]H subcluster, but also the di-iron centre. Enzyme in the H(trans) state reacts with extrinsic CO, which binds to Fe2. The H(trans) state converts irreversibly into the H(ox) state in a redox-dependent reaction most likely involving two electrons (E (m, pH 7) = -261 mV). These electrons do not end up on any of the six Fe atoms of the H cluster; the possible destiny of the two redox equivalents is discussed. An additional reversible one-electron redox reaction leads to the H(red) state (E (m, pH 7) = -354 mV), where both Fe atoms of the [2Fe]H subcluster have the same formal oxidation state. The possible oxidation states of Fe1 and Fe2 in the various enzyme states are discussed. Low redox potentials (below -500 mV) lead to destruction of the [2Fe]H subcluster.
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Affiliation(s)
- Winfried Roseboom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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9
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Albracht SPJ, Roseboom W, Hatchikian EC. The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. I. Light sensitivity and magnetic hyperfine interactions as observed by electron paramagnetic resonance. J Biol Inorg Chem 2005; 11:88-101. [PMID: 16323020 DOI: 10.1007/s00775-005-0039-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 09/26/2005] [Indexed: 10/25/2022]
Abstract
The hydrogen-activating cluster (H cluster) in [FeFe]-hydrogenases consists of two moieties. The [2Fe]H subcluster is a (L)(CO)(CN)Fe(mu-RS2)(mu-CO)Fe(CysS)(CO)(CN) centre. The Cys-bound Fe is called Fe1, the other iron Fe2. The Cys-thiol forms a bridge to a [4Fe-4S] cluster, the [4Fe-4S]H subcluster. We report that electron paramagnetic resonance (EPR) spectra of the 57Fe-enriched enzyme from Desulfovibrio desulfuricans in the H(ox)-CO state are consistent with a magnetic hyperfine interaction of the unpaired spin with all six Fe atoms of the H cluster. In contrast to the inactive aerobic enzyme, the active enzyme is easily destroyed by light. The [2Fe]H subcluster in some enzyme molecules loses CO by photolysis, whereupon other molecules firmly bind the released CO to form the H(ox)-CO state giving rise to the so-called axial 2.06 EPR signal. Though not destroyed by light, the H(ox)-CO state is affected by it. As demonstrated in the accompanying paper [49] two of the intrinsic COs, both bound to Fe2, can be exchanged by extrinsic 13CO during illumination at 2 degrees C. We found that only one of the three 13COs, the one at the extrinsic position, gives an EPR-detectable isotropic superhyperfine interaction of 0.6 mT. At 30 K both the inhibiting extrinsic CO bound to Fe2 and one more CO can be photolysed. EPR spectra of the photolysed products are consistent with a 3d7 system of Fe with the formal oxidation state +1. The damaged enzyme shows a light-sensitive g = 5 signal which is ascribed to an S = 3/2 form of the [2Fe](H) subcluster. The light sensitivity of the enzyme explains the occurrence of the g = 5 signal and the axial 2.06 signal in published EPR spectra of nearly all preparations studied thus far.
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Affiliation(s)
- Simon P J Albracht
- Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands,
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10
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Girbal L, von Abendroth G, Winkler M, Benton PMC, Meynial-Salles I, Croux C, Peters JW, Happe T, Soucaille P. Homologous and heterologous overexpression in Clostridium acetobutylicum and characterization of purified clostridial and algal Fe-only hydrogenases with high specific activities. Appl Environ Microbiol 2005; 71:2777-81. [PMID: 15870373 PMCID: PMC1087525 DOI: 10.1128/aem.71.5.2777-2781.2005] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium acetobutylicum ATCC 824 was selected for the homologous overexpression of its Fe-only hydrogenase and for the heterologous expressions of the Chlamydomonas reinhardtii and Scenedesmus obliquus HydA1 Fe-only hydrogenases. The three Strep tag II-tagged Fe-only hydrogenases were isolated with high specific activities by two-step column chromatography. The purified algal hydrogenases evolve hydrogen with rates of around 700 micromol H(2) min(-1) mg(-1), while HydA from C. acetobutylicum (HydA(Ca)) shows the highest activity (5,522 micromol H(2) min(-1) mg(-1)) in the direction of hydrogen uptake. Further, kinetic parameters and substrate specificity were reported. An electron paramagnetic resonance (EPR) analysis of the thionin-oxidized HydA(Ca) protein indicates a characteristic rhombic EPR signal that is typical for the oxidized H cluster of Fe-only hydrogenases.
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Affiliation(s)
- Laurence Girbal
- Laboratoire de Biotechnologie-Bioprocédés, UMR CNRS 5504, UMR INRA 792, INSA, 135 Avenue de Rangueil, 31077 Toulouse Cédex 4, France.
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11
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The iron-sulfur composition of the active site of hydrogenase fromDesulfovibrio vulgaris(Hildenborough) deduced from its subunit structure and total iron-sulfur content. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)81436-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Abstract
Biological nitrogen fixation is catalyzed by the nitrogenase enzyme system which consists of two metalloproteins, the iron (Fe-) protein and the molybdenum-iron (MoFe-) protein. Together, these proteins mediate the ATP-dependent reduction of dinitrogen to ammonia. Recent crystallographic analyses of Fe-protein and MoFe-protein have revealed the polypeptide fold and the structure and organization of the unusual metal centers in nitrogenase. These structure provide a molecular framework for addressing the mechanism of the nitrogenase-catalyzed reaction. General features of the nitrogenase system, including conformational coupling of nucleotide hydrolysis, aspects of the cluster structures, and the general spatial organization of redox centers within the protein subunits, are relevant to a wide range of biochemical systems.
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Affiliation(s)
- J Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125
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13
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Abstract
Hydrogenases devoid of nickel and containing only Fe-S clusters have been found so far only in some strictly anaerobic bacteria. Four Fe-hydrogenases have been characterized: from Megasphaera elsdenii, Desulfovibrio vulgaris (strain Hildenborough), and two from Clostridium pasteurianum. All contain two or more [4Fe-4S]1+,2+ or F clusters and a unique type of Fe-S center termed the H cluster. The H cluster appears to be remarkably similar in all the hydrogenases, and is proposed as the site of H2 oxidation and H2 production. The F clusters serve to transfer electrons between the H cluster and the external electron carrier. In all of the hydrogenases the H cluster is comprised of at least three Fe atoms, and possibly six. In the oxidized state it contains two types of magnetically distinct Fe atoms, has an S = 1/2 spin state, and exhibits a novel rhombic EPR signal. The reduced cluster is diamagnetic (S = 0). The oxidized H cluster appears to undergo a conformation change upon reduction with H2 with an increase in Fe-Fe distances of about 0.5 A. Studies using resonance Raman, magnetic circular dichroism and electron spin echo spectroscopies suggest that the H cluster has significant non-sulfur coordination. The H cluster has two binding sites for CO, at least one of which can also bind O2. Binding to one site changes the EPR properties of the cluster and gives a photosensitive adduct, but does not affect catalytic activity. Binding to the other site, which only becomes exposed during the catalytic cycle, leads to loss of catalytic activity. Mechanisms of H2 activation and electron transfer are proposed to explain the effects of CO binding and the ability of one of the hydrogenases to preferentially catalyze H2 oxidation.
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Affiliation(s)
- M W Adams
- Department of Biochemistry, University of Georgia, Athens 30602
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14
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Adams MW. The metabolism of hydrogen by extremely thermophilic, sulfur-dependent bacteria. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb04096.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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15
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16
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Zambrano IC, Kowal AT, Mortenson LE, Adams MW, Johnson MK. Magnetic Circular Dichroism and Electron Paramagnetic Resonance Studies of Hydrogenases I and II from Clostridium pasteurianum. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)30032-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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17
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Filipiak M, Hagen WR, Veeger C. Hydrodynamic, structural and magnetic properties of Megasphaera elsdenii Fe hydrogenase reinvestigated. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 185:547-53. [PMID: 2556270 DOI: 10.1111/j.1432-1033.1989.tb15148.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Megasphaera elsdenii hydrogenase has been purified to homogeneity using an FPLC procedure as the final step. The protein gives a single band in SDS/PAGE with an apparent molecular mass of 57-59 kDa. There is no second hydrogenase activity in the soluble fraction of M. elsdenii. The hydrodynamics of the enzyme have been compared to those of the two-subunit Fe hydrogenase from Desulfovibrio vulgaris (Hildenborough) in the analytical ultracentrifuge using the absorption of the intrinsic iron-sulfur clusters as the monitor. Sedimentation-velocity experiments indicate the M. elsdenii enzyme (s20,w = 4.95 S) to be essentially globular, while the D. vulgaris enzyme (s20,w = 4.1 S) has a less symmetric shape. From the sedimentation equilibrium measurements under a variety of conditions an average molecular mass is calculated of 58 kDa (M. elsdenii) and 54 kDa (D. vulgaris), respectively. Pure, maximally active M. elsdenii hydrogenase has A405/A280 = 0.36 and has a specific H2-production activity of 400 mumol H2.min-1.(mg protein)-1 at 30 degrees C and pH 8.0. The enzyme contains some 13-18 iron and acid-labile sulfur ions/58-kDa monomer. Eight of these Fe-S are present as two electron-transferring ferredoxin-like cubanes with Em approximately greater than -0.3 V, as indicated by pH-dependent EPR spectroscopy on the H2-reduced enzyme. In the (re)oxidized state the remainder iron gives rise to a single S = 1/2 rhombic EPR signal. Hydrogen-production activity, content of remainder iron and rhombic EPR signal intensity are mutually correlated. Purified hydrogenase appears to exist as a mixture of fully active holoenzyme and inactive protein still carrying the two cubanes but deficient in active-site iron.
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Affiliation(s)
- M Filipiak
- Department of Biochemistry, Agricultural University, Wageningen, The Netherlands
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18
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Adams MW, Eccleston E, Howard JB. Iron-sulfur clusters of hydrogenase I and hydrogenase II of Clostridium pasteurianum. Proc Natl Acad Sci U S A 1989; 86:4932-6. [PMID: 2544883 PMCID: PMC297529 DOI: 10.1073/pnas.86.13.4932] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The iron and acid-labile sulfide contents and the electron paramagnetic resonance (EPR) properties of hydrogenase I (bidirectional) and hydrogenase II (uptake) of Clostridium pasteurianum (strain W5) have been determined on the basis of quantitative amino acid analyses. The iron and acid-labile sulfide values are approximately 20 and 18 atoms per molecule of hydrogenase I and 14 and 11 atoms per molecule of hydrogenase II, respectively. These amounts are substantially greater than previously reported values, which relied on protein concentration determined by colorimetric assay. The oxidized hydrogenases exhibit unusual EPR signals that originate from a novel type of iron-sulfur center, termed the hydrogenase or H cluster, which covalently binds the inhibitor CO. This EPR signal represents approximately one unpaired electron per molecule in each enzyme with and without bound CO, which is consistent with the presence of one oxidized H cluster (S = 1/2) per enzyme molecule. The two enzymes also contain ferredoxin-type four-iron centers or F clusters. The EPR signals from the F clusters observed in the reduced forms of hydrogenase I and hydrogenase II account for approximately four and one unpaired electron per molecule, respectively. We conclude from the iron determinations and the EPR results, together with a reevaluation of previous spectroscopic data, that in both hydrogenases the H cluster probably comprises six iron atoms. Mechanistic models of the two hydrogenases are presented that account for their cluster compositions and the dramatic differences in their catalytic activities.
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Affiliation(s)
- M W Adams
- Department of Biochemistry, School of Chemical Sciences, University of Georgia, Athens 30602
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Cammack R, Kovacs KL, McCracken J, Peisach J. Spectroscopic characterization of the nickel and iron-sulphur clusters of hydrogenase from the purple photosynthetic bacterium Thiocapsa roseopersicina. 2. Electron spin-echo spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 182:363-6. [PMID: 2544425 DOI: 10.1111/j.1432-1033.1989.tb14839.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pulsed electron-spin-resonance techniques were applied to the hydrogenase of the purple photosynthetic bacterium Thiocapsa roseopersicina, an enzyme which contains nickel and iron-sulphur clusters but no flavin. The linear electric field effect profile of the spectrum in the region of g = 2.01 indicated that the strong ESR signal in the oxidized protein is due to a [3Fe-4S] cluster. The electron spin-echo envelope of this spectrum was modulated by hyperfine interactions with 1H and 14N nuclei, probably from the polypeptide chain. The ESR spectrum of this species shows a complex pattern arising from spin-spin interaction with another paramagnet. When the protein was partially reduced by ascorbate plus phenazine methosulphate, the complexity of the spectrum was abolished but the form of the electron spin-echo envelope modulation (ESEEM) pattern was unchanged. This indicates that the reversible disappearance of the spin-spin interaction pattern on partial reduction is not due to cluster interconversion to a [4Fe-4S] cluster. In the ESR spectrum of nickel(III), weak hyperfine interactions with 1H and 14N were also observed by ESEEM. The nature of the interacting nuclei is discussed.
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Affiliation(s)
- R Cammack
- Department of Biochemistry, King's College, London, England
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20
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George GN, Prince RC, Stokley KE, Adams MW, Stockley KE. X-ray-absorption-spectroscopic evidence for a novel iron cluster in hydrogenase II from Clostridium pasteurianum. Biochem J 1989; 259:597-600. [PMID: 2655584 PMCID: PMC1138551 DOI: 10.1042/bj2590597] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hydrogenase II from Clostridium pasteurianum contains three different iron-sulphur clusters. Two are [4Fe-4S](2+.1+) clusters, whereas the other, which is thought to be the site of interaction with H2 and is known as the 'H cluster', is of unknown structure and possesses unusual spectroscopic properties. Analysis of the iron e.x.a.f.s. spectra shows that the H cluster contains iron co-ordinated mostly to sulphur and possesses 2.8 A (1 A = 0.1 nm) Fe--Fe separations when oxidized and 3.3 A Fe--Fe separations when reduced with H2. The data suggest that the reduced H cluster represents a new structural type of iron-sulphur cluster.
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Affiliation(s)
- G N George
- EXXON Research & Engineering Co., Annandale, NJ 08801
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21
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Bryant FO, Adams MW. Characterization of Hydrogenase from the Hyperthermophilic Archaebacterium, Pyrococcus furiosus. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83701-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Kowal AT, Adams MW, Johnson MK. Electron paramagnetic resonance studies of the low temperature photolytic behavior of oxidized hydrogenase I from Clostridium pasteurianum. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83747-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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23
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Knüttel K, Schneider K, Schlegel HG, Müller A. The membrane-bound hydrogenase from Paracoccus denitrificans. Purification and molecular characterization. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 179:101-8. [PMID: 2537196 DOI: 10.1111/j.1432-1033.1989.tb14526.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The membrane-bound hydrogenase from Paracoccus denitrificans was purified 68-fold with a yield of 14.6%. The final preparation had a specific activity of 161.9 mumol H2 min-1 (mg protein)-1 (methylene blue reduction). Purification involved solubilization by Triton X-114, phase separation, chromatography on DEAE-Sephacel, ammonium-sulfate precipitation and chromatography on Procion-red HE-3B-Sepharose. Gel electrophoresis under denaturing conditions revealed two non-identical subunits with molecular masses of 64 kDa and 34 kDa. The molecular mass of the native enzyme was 100 kDa, as estimated by FPLC gel filtration in the presence of Chaps, a zwitterionic detergent. The isoelectric point of the Paracoccus hydrogenase was 4.3. Metal analysis of the purified enzyme indicated a content of 0.6 nickel and 7.3 iron atoms/molecule. ESR spectra of the reduced enzyme exhibited a close similarity to the membrane-bound hydrogenase from Alcaligenes eutrophus H16 with g values of 1.86, 1.92 and 1.98. The half-life for inactivation under air at 20 degrees C was 8 h. The Paracoccus hydrogenase reduced several electron acceptors, namely methylene blue, benzyl viologen, methyl viologen, menadione, cytochrome c, FMN, 2,6-dichloroindophenol, ferricyanide and phenazine methosulfate. The highest activity was measured with methylene blue (V = 161.9 U/mg; Km = 0.04 mM), whereas benzyl and methyl viologen were reduced at distinctly lower rates (16.5 U/mg and 12.1 U/mg, respectively). The native hydrogenase from P. denitrificans cross-reacted with purified antibodies raised against the membrane-bound hydrogenase from A. eutrophus H16. The corresponding subunits from both enzymes also showed immunological relationship. All reactions were of partial identity.
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Affiliation(s)
- K Knüttel
- Institut für Mikrobiologie der Universität Göttingen, Federal Republic of Germany
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24
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Fauque G, Peck HD, Moura JJ, Huynh BH, Berlier Y, DerVartanian DV, Teixeira M, Przybyla AE, Lespinat PA, Moura I. The three classes of hydrogenases from sulfate-reducing bacteria of the genus Desulfovibrio. FEMS Microbiol Rev 1988; 4:299-344. [PMID: 3078655 DOI: 10.1111/j.1574-6968.1988.tb02748.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Three types of hydrogenases have been isolated from the sulfate-reducing bacteria of the genus Desulfovibrio. They differ in their subunit and metal compositions, physico-chemical characteristics, amino acid sequences, immunological reactivities, gene structures and their catalytic properties. Broadly, the hydrogenases can be considered as 'iron only' hydrogenases and nickel-containing hydrogenases. The iron-sulfur-containing hydrogenase ([Fe] hydrogenase) contains two ferredoxin-type (4Fe-4S) clusters and an atypical iron-sulfur center believed to be involved in the activation of H2. The [Fe] hydrogenase has the highest specific activity in the evolution and consumption of hydrogen and in the proton-deuterium exchange reaction and this enzyme is the most sensitive to CO and NO2-. It is not present in all species of Desulfovibrio. The nickel-(iron-sulfur)-containing hydrogenases [( NiFe] hydrogenases) possess two (4Fe-4S) centers and one (3Fe-xS) cluster in addition to nickel and have been found in all species of Desulfovibrio so far investigated. The redox active nickel is ligated by at least two cysteinyl thiolate residues and the [NiFe] hydrogenases are particularly resistant to inhibitors such as CO and NO2-. The genes encoding the large and small subunits of a periplasmic and a membrane-bound species of the [NiFe] hydrogenase have been cloned in Escherichia (E.) coli and sequenced. Their derived amino acid sequences exhibit a high degree of homology (70%); however, they show no obvious metal-binding sites or homology with the derived amino acid sequence of the [Fe] hydrogenase. The third class is represented by the nickel-(iron-sulfur)-selenium-containing hydrogenases [( NiFe-Se] hydrogenases) which contain nickel and selenium in equimolecular amounts plus (4Fe-4S) centers and are only found in some species of Desulfovibrio. The genes encoding the large and small subunits of the periplasmic hydrogenase from Desulfovibrio (D.) baculatus (DSM 1743) have been cloned in E. coli and sequenced. The derived amino acid sequence exhibits homology (40%) with the sequence of the [NiFe] hydrogenase and the carboxy-terminus of the gene for the large subunit contains a codon (TGA) for selenocysteine in a position homologous to a codon (TGC) for cysteine in the large subunit of the [NiFe] hydrogenase. EXAFS and EPR studies with the 77Se-enriched D. baculatus hydrogenase indicate that selenium is a ligand to nickel and suggest that the redox active nickel is ligated by at least two cysteinyl thiolate and one selenocysteine selenolate residues.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- G Fauque
- Section Enzymologie et Biochimie Bactérienne, ARBS, CEN Cadarache, Saint-Paul-Lez-Durance, France
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Adams MW. The mechanisms of H2 activation and CO binding by hydrogenase I and hydrogenase II of Clostridium pasteurianum. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)48137-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Macor K, Czernuszewicz R, Adams M, Spiro T. An investigation of hydrogenase I and hydrogenase II from Clostridium pasteurianum by resonance Raman spectroscopy. Evidence for a [2Fe-2S] cluster in hydrogenase I. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61056-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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27
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EPR and electron nuclear double resonance investigation of oxidized hydrogenase II (uptake) from Clostridium pasteurianum W5. Effects of carbon monoxide binding. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)48282-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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28
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Schindler F, Winter J. Purification and properties of a soluble, thermophilic hydrogenase of Acetomicrobium flavidum. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0167-4838(87)90235-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Rusnak FM, Adams MW, Mortenson LE, Münck E. Mössbauer study of Clostridium pasteurianum hydrogenase II. Evidence for a novel three-iron cluster. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(19)75883-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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30
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Telser J, Benecky MJ, Adams MW, Mortenson LE, Hoffman BM. An EPR and electron nuclear double resonance investigation of carbon monoxide binding to hydrogenase I (bidirectional) from Clostridium pasteurianum W5. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67051-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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