1
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Lewis LC, Sanabria-Gracia JA, Lee Y, Jenkins AJ, Shafaat HS. Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase. Chem Sci 2024; 15:5916-5928. [PMID: 38665523 PMCID: PMC11040638 DOI: 10.1039/d4sc00023d] [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: 01/02/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024] Open
Abstract
The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme uses a heterometallic nickel-iron-sulfur ([NiFe4S4]) cluster to catalyze the reversible interconversion of carbon dioxide (CO2) and carbon monoxide (CO). These reactions are essential for maintaining the global carbon cycle and offer a route towards sustainable greenhouse gas conversion but have not been successfully replicated in synthetic models, in part due to a poor understanding of the natural system. Though the general protein architecture of CODH is known, the electronic structure of the active site is not well-understood, and the mechanism of catalysis remains unresolved. To better understand the CODH enzyme, we have developed a protein-based model containing a heterometallic [NiFe3S4] cluster in the Pyrococcus furiosus (Pf) ferredoxin (Fd). This model binds small molecules such as carbon monoxide and cyanide, analogous to CODH. Multiple redox- and ligand-bound states of [NiFe3S4] Fd (NiFd) have been investigated using a suite of spectroscopic techniques, including resonance Raman, Ni and Fe K-edge X-ray absorption spectroscopy, and electron paramagnetic resonance, to resolve charge and spin delocalization across the cluster, site-specific electron density, and ligand activation. The facile movement of charge through the cluster highlights the fluidity of electron density within iron-sulfur clusters and suggests an electronic basis by which CN- inhibits the native system while the CO-bound state continues to elude isolation in CODH. The detailed characterization of isolable states that are accessible in our CODH model system provides valuable insight into unresolved enzymatic intermediates and offers design principles towards developing functional mimics of CODH.
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Affiliation(s)
- Luke C Lewis
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - José A Sanabria-Gracia
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - Yuri Lee
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles CA 90095 USA
| | - Adam J Jenkins
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles CA 90095 USA
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2
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Ruickoldt J, Basak Y, Domnik L, Jeoung JH, Dobbek H. On the Kinetics of CO 2 Reduction by Ni, Fe-CO Dehydrogenases. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakob Ruickoldt
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Yudhajeet Basak
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Lilith Domnik
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Jae-Hun Jeoung
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
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3
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Basak Y, Jeoung JH, Domnik L, Ruickoldt J, Dobbek H. Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yudhajeet Basak
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Jae-Hun Jeoung
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Lilith Domnik
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Jakob Ruickoldt
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Holger Dobbek
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
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4
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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5
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Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism. Catalysts 2022. [DOI: 10.3390/catal12020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.
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6
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Breglia R, Arrigoni F, Sensi M, Greco C, Fantucci P, De Gioia L, Bruschi M. First-Principles Calculations on Ni,Fe-Containing Carbon Monoxide Dehydrogenases Reveal Key Stereoelectronic Features for Binding and Release of CO 2 to/from the C-Cluster. Inorg Chem 2020; 60:387-402. [PMID: 33321036 PMCID: PMC7872322 DOI: 10.1021/acs.inorgchem.0c03034] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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In view of the depletion of fossil
fuel reserves and climatic effects
of greenhouse gas emissions, Ni,Fe-containing carbon monoxide dehydrogenase
(Ni-CODH) enzymes have attracted increasing interest in recent years
for their capability to selectively catalyze the reversible reduction
of CO2 to CO (CO2 + 2H+ + 2e– CO + H2O). The possibility of
converting the greenhouse gas CO2 into useful materials
that can be used as synthetic building blocks or, remarkably, as carbon
fuels makes Ni-CODH a very promising target for reverse-engineering
studies. In this context, in order to provide insights into the chemical
principles underlying the biological catalysis of CO2 activation
and reduction, quantum mechanics calculations have been carried out
in the framework of density functional theory (DFT) on different-sized
models of the Ni-CODH active site. With the aim of uncovering which
stereoelectronic properties of the active site (known as the C-cluster)
are crucial for the efficient binding and release of CO2, different coordination modes of CO2 to different forms
and redox states of the C-cluster have been investigated. The results
obtained from this study highlight the key role of the protein environment
in tuning the reactivity and the geometry of the C-cluster. In particular,
the protonation state of His93 is found to be crucial for promoting
the binding or the dissociation of CO2. The oxidation state
of the C-cluster is also shown to be critical. CO2 binds
to Cred2 according to a dissociative mechanism (i.e., CO2 binds to the C-cluster after the release of possible ligands
from Feu) when His93 is doubly protonated. CO2 can also bind noncatalytically to Cred1 according to
an associative mechanism (i.e., CO2 binding is preceded
by the binding of H2O to Feu). Conversely, CO2 dissociates when His93 is singly protonated and the C-cluster
is oxidized at least to the Cint redox state. Density functional theory was used to investigate Ni,Fe-containing
carbon monoxide dehydrogenase enzymes. Different coordination modes
of the substrate CO2 to several forms and redox states
of the C-cluster—the enzyme active site—were considered.
The obtained results highlight the key role of the protein environment
in tuning the reactivity and the geometry of the C-cluster. This helps
to uncover which stereoelectronic properties of the active site are
crucial for the efficient binding and release of CO2.
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Affiliation(s)
- Raffaella Breglia
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Matteo Sensi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Maurizio Bruschi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
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7
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Abstract
Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of CO with water to CO2, two electrons, and two protons. Two classes of CODHs exist, having evolved from different scaffolds featuring active sites built from different transition metals. The basic properties of both classes are described in this overview chapter.
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Affiliation(s)
- Jae-Hun Jeoung
- Institute of Biology, Structural Biology and Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Berta M Martins
- Institute of Biology, Structural Biology and Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Holger Dobbek
- Institute of Biology, Structural Biology and Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany.
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8
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Wittenborn EC, Merrouch M, Ueda C, Fradale L, Léger C, Fourmond V, Pandelia ME, Dementin S, Drennan CL. Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase. eLife 2018; 7:39451. [PMID: 30277213 PMCID: PMC6168284 DOI: 10.7554/elife.39451] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/23/2018] [Indexed: 01/03/2023] Open
Abstract
The C-cluster of the enzyme carbon monoxide dehydrogenase (CODH) is a structurally distinctive Ni-Fe-S cluster employed to catalyze the reduction of CO2 to CO as part of the Wood-Ljungdahl carbon fixation pathway. Using X-ray crystallography, we have observed unprecedented conformational dynamics in the C-cluster of the CODH from Desulfovibrio vulgaris, providing the first view of an oxidized state of the cluster. Combined with supporting spectroscopic data, our structures reveal that this novel, oxidized cluster arrangement plays a role in avoiding irreversible oxidative degradation at the C-cluster. Furthermore, mutagenesis of a conserved cysteine residue that binds the C-cluster in the oxidized state but not in the reduced state suggests that the oxidized conformation could be important for proper cluster assembly, in particular Ni incorporation. Together, these results lay a foundation for future investigations of C-cluster activation and assembly, and contribute to an emerging paradigm of metallocluster plasticity.
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Affiliation(s)
- Elizabeth C Wittenborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Mériem Merrouch
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Chie Ueda
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Laura Fradale
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Christophe Léger
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Vincent Fourmond
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | | | - Sébastien Dementin
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Canada
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9
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Sultana S, Chandra Sahoo P, Martha S, Parida K. A review of harvesting clean fuels from enzymatic CO2 reduction. RSC Adv 2016. [DOI: 10.1039/c6ra05472b] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This review has summarised single enzyme, multi enzymatic and semiconducting nanomaterial integrated enzymatic systems for CO2 conversion to clean fuels.
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Affiliation(s)
- Sabiha Sultana
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Prakash Chandra Sahoo
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Satyabadi Martha
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Kulamani Parida
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
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10
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Wang VCC, Can M, Pierce E, Ragsdale SW, Armstrong FA. A unified electrocatalytic description of the action of inhibitors of nickel carbon monoxide dehydrogenase. J Am Chem Soc 2013; 135:2198-206. [PMID: 23368960 PMCID: PMC3894609 DOI: 10.1021/ja308493k] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Several small molecules and ions, notably carbon monoxide, cyanide, cyanate, and hydrogen sulfide, are potent inhibitors of Ni-containing carbon monoxide dehydrogenases (Ni-CODH) that catalyze very rapid, efficient redox interconversions of CO(2) and CO. Protein film electrochemistry, which probes the dependence of steady-state catalytic rate over a wide potential range, reveals how these inhibitors target particular oxidation levels of Ni-CODH relating to intermediates (C(ox), C(red1), and C(red2)) that have been established for the active site. The following properties are thus established: (1) CO suppresses CO(2) reduction (CO is a product inhibitor), but its binding affinity decreases as the potential becomes more negative. (2) Cyanide totally inhibits CO oxidation, but its effect on CO(2) reduction is limited to a narrow potential region (between -0.5 and -0.6 V), below which CO(2) reduction activity is restored. (3) Cyanate is a strong inhibitor of CO(2) reduction but inhibits CO oxidation only within a narrow potential range just above the CO(2)/CO thermodynamic potential--EPR spectra confirm that cyanate binds selectively to C(red2). (4) Hydrogen sulfide (H(2)S/HS(-)) inhibits CO oxidation but not CO(2) reduction--the complex on/off characteristics are consistent with it binding at the same oxidation level as C(ox) and forming a modified version of this inactive state rather than reacting directly with C(red1). The results provide a new perspective on the properties of different catalytic intermediates of Ni-CODH--uniting and clarifying many previous investigations.
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Affiliation(s)
- Vincent C.-C. Wang
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Park Road, Oxford OX1 3QR, U.K
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, United States
| | - Elizabeth Pierce
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, United States
| | - Fraser A. Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Park Road, Oxford OX1 3QR, U.K
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11
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CAO ZEXING, MO YIRONG. COMPUTATIONAL CHARACTERIZATION OF THE ELUSIVE C-CLUSTER OF CARBON MONOXIDE DEHYDROGENASE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608003903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Structural features of the C-cluster of carbon monoxide dehydrogenases at different redox states have been investigated by the density functional theory. The key species involved in the oxidation of CO at clusters C , Cox, Cred1, Cred2, and Cint, have been specified. Computational results indicate that the CO -induced transformation of the [Ni–4Fe–5S] cluster C into the [Ni–4Fe–4S] cluster is facile energetically, and such structural conversion at the active site may reconcile different reported crystal structures of cluster C. The coordination of CO to the Ni site of the reduced C-cluster (Cred1) will enhance its electron accommodation ability and makes Fe1 more accessible to other substrates, which lends support to the assumption that Cred1is a ready state for CO oxidation. On the basis of calculations, the possible catalytic cycle for the oxidation of CO at cluster C was proposed.
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Affiliation(s)
- ZEXING CAO
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China
| | - YIRONG MO
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
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12
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Zhu X, Tan X. Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0082-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Seravalli J, Ragsdale SW. 13C NMR characterization of an exchange reaction between CO and CO2 catalyzed by carbon monoxide dehydrogenase. Biochemistry 2008; 47:6770-81. [PMID: 18589895 PMCID: PMC2664834 DOI: 10.1021/bi8004522] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 04/21/2008] [Indexed: 11/30/2022]
Abstract
Carbon monoxide dehydrogenase (CODH) catalyzes the reversible oxidation of CO to CO2 at a nickel-iron-sulfur cluster (the C-cluster). CO oxidation follows a ping-pong mechanism involving two-electron reduction of the C-cluster followed by electron transfer through an internal electron transfer chain to external electron acceptors. We describe 13C NMR studies demonstrating a CODH-catalyzed steady-state exchange reaction between CO and CO2 in the absence of external electron acceptors. This reaction is characterized by a CODH-dependent broadening of the 13CO NMR resonance; however, the chemical shift of the 13CO resonance is unchanged, indicating that the broadening is in the slow exchange limit of the NMR experiment. The 13CO line broadening occurs with a rate constant (1080 s-1 at 20 degrees C) that is approximately equal to that of CO oxidation. It is concluded that the observed exchange reaction is between 13CO and CODH-bound 13CO2 because 13CO line broadening is pH-independent (unlike steady-state CO oxidation), because it requires a functional C-cluster (but not a functional B-cluster) and because the 13CO2 line width does not broaden. Furthermore, a steady-state isotopic exchange reaction between 12CO and 13CO2 in solution was shown to occur at the same rate as that of CO2 reduction, which is approximately 750-fold slower than the rate of 13CO exchange broadening. The interaction between CODH and the inhibitor cyanide (CN-) was also probed by 13C NMR. A functional C-cluster is not required for 13CN- broadening (unlike for 13CO), and its exchange rate constant is 30-fold faster than that for 13CO. The combined results indicate that the 13CO exchange includes migration of CO to the C-cluster, and CO oxidation to CO2, but not release of CO2 or protons into the solvent. They also provide strong evidence of a CO2 binding site and of an internal proton transfer network in CODH. 13CN- exchange appears to monitor only movement of CN- between solution and its binding to and release from CODH.
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Affiliation(s)
| | - Stephen W. Ragsdale
- To whom correspondence should be addressed: Department of Biological Chemistry, University of Michigan, University of Michigan Medical School, 5301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-0606. Phone:
(734) 615-4621
. Fax: (734) 763-4581. E-mail:
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14
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Lindahl P. Kohlenmonoxid-Dehydrogenasen: Implikationen einer C-Clusterstruktur mit gebundenem Carboxylat. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Lindahl P. Implications of a Carboxylate-Bound C-Cluster Structure of Carbon Monoxide Dehydrogenase. Angew Chem Int Ed Engl 2008; 47:4054-6. [DOI: 10.1002/anie.200800223] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Jeoung JH, Dobbek H. Carbon dioxide activation at the Ni,Fe-cluster of anaerobic carbon monoxide dehydrogenase. Science 2007; 318:1461-4. [PMID: 18048691 DOI: 10.1126/science.1148481] [Citation(s) in RCA: 401] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Anaerobic CO dehydrogenases catalyze the reversible oxidation of CO to CO2 at a complex Ni-, Fe-, and S-containing metal center called cluster C. We report crystal structures of CO dehydrogenase II from Carboxydothermus hydrogenoformans in three different states. In a reduced state, exogenous CO2 supplied in solution is bound and reductively activated by cluster C. In the intermediate structure, CO2 acts as a bridging ligand between Ni and the asymmetrically coordinated Fe, where it completes the square-planar coordination of the Ni ion. It replaces a water/hydroxo ligand bound to the Fe ion in the other two states. The structures define the mechanism of CO oxidation and CO2 reduction at the Ni-Fe site of cluster C.
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Affiliation(s)
- Jae-Hun Jeoung
- Laboratorium Proteinkristallographie and Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, D-95440 Bayreuth, Germany
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17
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Shin W, Lee SH, Shin JW, Lee SP, Kim Y. Highly selective electrocatalytic conversion of CO2 to CO at -0.57 V (NHE) by carbon monoxide dehydrogenase from Moorella thermoacetica. J Am Chem Soc 2004; 125:14688-9. [PMID: 14640627 DOI: 10.1021/ja037370i] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We found that CODH is a fascinating enzyme for the electrochemical conversion of CO2 to CO. It could reduce CO2 to CO at -0.57 V vs NHE with approximately 100% current efficiency in 0.1 M phosphate buffer (pH 6.3). Nature's unique structure of C-cluster in CODH would be responsible for the low overpotential and the selective and fast conversion of CO2. The turnover number per C-cluster is 700 h-1, and the pH optimum is 6.3.
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Affiliation(s)
- Woonsup Shin
- Department of Chemistry, Sogang University, Seoul 121-742, Korea
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Metzler DE, Metzler CM, Sauke DJ. Transition Metals in Catalysis and Electron Transport. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Loke HK, Bennett GN, Lindahl PA. Active acetyl-CoA synthase from Clostridium thermoaceticum obtained by cloning and heterologous expression of acsAB in Escherichia coli. Proc Natl Acad Sci U S A 2000; 97:12530-5. [PMID: 11050160 PMCID: PMC18798 DOI: 10.1073/pnas.220404397] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetyl-CoA synthase from Clostridium thermoaceticum (ACS(Ct)) is an alpha(2)beta(2) tetramer containing two novel Ni-X-Fe(4)S(4) active sites (the A and C clusters) and a standard Fe(4)S(4) cluster (the B cluster). The acsA and acsB genes encoding the enzyme were cloned into Escherichia coli strain JM109 and overexpressed at 37(o)C under anaerobic conditions with Ni supplementation. The isolated recombinant His-tagged protein (AcsAB) exhibited characteristics essentially indistinguishable from those of ACS(Ct), from which Ni had been removed from the A cluster. AcsAB migrated through nondenaturing electrophoretic gels as a single band and contained a 1:1 molar ratio of subunits and 1.0-1.6 Ni/alphabeta and 14-22 Fe/alphabeta. AcsAB exhibited 100-250 units/mg CO oxidation activity but no CO/acetyl-CoA exchange activity. Electronic absorption spectra of thionin-oxidized and CO-reduced AcsAB were similar to those of ACS(Ct), with features typical of redox-active Fe(4)S(4) clusters. Partially oxidized and CO-reduced AcsAB exhibited EPR signals with g values and low spin intensities indistinguishable from those of the B(red) state of the B cluster and the C(red1) and C(red2) states of the C cluster of ACS(Ct). Upon overnight exposure to NiCl(2), the resulting recombinant enzyme (ACS(Ec)) developed 0. 06-0.25 units/mg exchange activity. The highest of these values is typical of fully active ACS(Ct). When reduced with CO, ACS(Ec) exhibited an EPR signal indistinguishable from the NiFeC signal of Ni-replete ACS(Ct). Variability of activities and signal intensities were observed among different preparations. Issues involving the assembly of these metal centers in E. coli are discussed.
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Affiliation(s)
- H K Loke
- Departments of Chemistry and Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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