1
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Newman-Stonebraker SH, Gerard TJ, Holland PL. Opportunities for Insight into the Mechanism of Efficient CO 2/CO Interconversion at a Nickel-Iron Cluster in CO Dehydrogenase. Chem 2024; 10:1655-1667. [PMID: 38966253 PMCID: PMC11221784 DOI: 10.1016/j.chempr.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The reduction of CO2 with low overpotential and high selectivity is a crucial challenge in catalysis. Fortunately, natural systems have evolved enzymes that achieve this catalytic reaction very efficiently at a complex nickel-iron-sulfur cluster within carbon monoxide dehydrogenase (CODH). Extensive biochemical, crystallographic, and spectroscopic work has been done to understand the structures and mechanism involved in the catalytic cycle, which are summarized here from the perspective of mechanistic organometallic chemistry. We highlight the ambiguities in the data and suggest experiments that could lead to clearer understanding of the mechanism and structures of intermediates at the active-site cluster. These include parallel crystallography and spectroscopy, as well as the preparation of synthetic analogues that help to interpret structural and spectroscopic signatures.
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2
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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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3
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Xiao Y, Xie F, Zhang HT, Zhang MT. Bioinspired Binickel Catalyst for Carbon Dioxide Reduction: The Importance of Metal-ligand Cooperation. JACS AU 2024; 4:1207-1218. [PMID: 38559717 PMCID: PMC10976602 DOI: 10.1021/jacsau.4c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 04/04/2024]
Abstract
Catalyst design for the efficient CO2 reduction reaction (CO2RR) remains a crucial challenge for the conversion of CO2 to fuels. Natural Ni-Fe carbon monoxide dehydrogenase (NiFe-CODH) achieves reversible conversion of CO2 and CO at nearly thermodynamic equilibrium potential, which provides a template for developing CO2RR catalysts. However, compared with the natural enzyme, most biomimetic synthetic Ni-Fe complexes exhibit negligible CO2RR catalytic activities, which emphasizes the significance of effective bimetallic cooperation for CO2 activation. Enlightened by bimetallic synergy, we herein report a dinickel complex, NiIINiII(bphpp)(AcO)2 (where NiNi(bphpp) is derived from H2bphpp = 2,9-bis(5-tert-butyl-2-hydroxy-3-pyridylphenyl)-1,10-phenanthroline) for electrocatalytic reduction of CO2 to CO, which exhibits a remarkable reactivity approximately 5 times higher than that of the mononuclear Ni catalyst. Electrochemical and computational studies have revealed that the redox-active phenanthroline moiety effectively modulates the electron injection and transfer akin to the [Fe3S4] cluster in NiFe-CODH, and the secondary Ni site facilitates the C-O bond activation and cleavage through electron mediation and Lewis acid characteristics. Our work underscores the significant role of bimetallic cooperation in CO2 reduction catalysis and provides valuable guidance for the rational design of CO2RR catalysts.
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Affiliation(s)
- Yao Xiao
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Fei Xie
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Hong-Tao Zhang
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ming-Tian Zhang
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
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4
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Yong WW, Zhang HT, Guo YH, Xie F, Zhang MT. Redox-Active Ligand Assisted Multielectron Catalysis: A Case of Electrocatalyzed CO 2-to-CO Conversion. ACS ORGANIC & INORGANIC AU 2023; 3:384-392. [PMID: 38075450 PMCID: PMC10704577 DOI: 10.1021/acsorginorgau.3c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 03/16/2024]
Abstract
The selective reduction of carbon dioxide remains a significant challenge due to the complex multielectron/proton transfer process, which results in a high kinetic barrier and the production of diverse products. Inspired by the electrostatic and H-bonding interactions observed in the second sphere of the [NiFe]-CODH enzyme, researchers have extensively explored these interactions to regulate proton transfer, stabilize intermediates, and ultimately improve the performance of catalytic CO2 reduction. In this work, a series of cobalt(II) tetraphenylporphyrins with varying numbers of redox-active nitro groups were synthesized and evaluated as CO2 reduction electrocatalysts. Analyses of the redox properties of these complexes revealed a consistent relationship between the number of nitro groups and the corresponding accepted electron number of the ligand at -1.59 V vs. Fc+/0. Among the catalysts tested, TNPPCo with four nitro groups exhibited the most efficient catalytic activity with a turnover frequency of 4.9 × 104 s-1 and a catalytic onset potential 820 mV more positive than that of the parent TPPCo. Furthermore, the turnover frequencies of the catalysts increased with a higher number of nitro groups. These results demonstrate the promising design strategy of incorporating multielectron redox-active ligands into CO2 reduction catalysts to enhance catalytic performance.
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Affiliation(s)
- Wen-Wen Yong
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
- Institute
of Materials, China Academy of Engineering Physics (CAEP), Jiangyou 621908, China
| | - Hong-Tao Zhang
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu-Hua Guo
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Fei Xie
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ming-Tian Zhang
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
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5
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Fujishiro T, Takaoka K. Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases. Nat Commun 2023; 14:5609. [PMID: 37709776 PMCID: PMC10502027 DOI: 10.1038/s41467-023-41289-4] [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: 06/12/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Hybrid cluster proteins (HCPs) are Fe-S-O cluster-containing metalloenzymes in three distinct classes (class I and II: monomer, III: homodimer), all of which structurally related to homodimeric Ni, Fe-carbon monoxide dehydrogenases (CODHs). Here we show X-ray crystal structure of class III HCP from Methanothermobacter marburgensis (Mm HCP), demonstrating its homodimeric architecture structurally resembles those of CODHs. Also, despite the different architectures of class III and I/II HCPs, [4Fe-4S] and hybrid clusters are found in equivalent positions in all HCPs. Structural comparison of Mm HCP and CODHs unveils some distinct features such as the environments of their homodimeric interfaces and the active site metalloclusters. Furthermore, structural analysis of Mm HCP C67Y and characterization of several Mm HCP variants with a Cys67 mutation reveal the significance of Cys67 in protein structure, metallocluster binding and hydroxylamine reductase activity. Structure-based bioinformatics analysis of HCPs and CODHs provides insights into the structural evolution of the HCP/CODH superfamily.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan.
| | - Kyosei Takaoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
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6
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Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
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Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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7
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Partipilo M, Claassens NJ, Slotboom DJ. A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells. ACS Synth Biol 2023; 12:947-962. [PMID: 37052416 PMCID: PMC10127272 DOI: 10.1021/acssynbio.3c00070] [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: 01/31/2023] [Indexed: 04/14/2023]
Abstract
The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.
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Affiliation(s)
- Michele Partipilo
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nico J. Claassens
- Laboratory
of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Jan Slotboom
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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8
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Biester A, Marcano-Delgado AN, Drennan CL. Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases. Biochemistry 2022; 61:2797-2805. [PMID: 36137563 PMCID: PMC9782325 DOI: 10.1021/acs.biochem.2c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ni-Fe-S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO2 by using their catalytic Ni-Fe-S C-cluster and their Fe-S B- and D-clusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO2 as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood-Ljungdahl pathway, where acetyl-CoA is assembled from two CO2-derived one-carbon units. A Ni-Fe-S A-cluster is key to this chemistry. Whereas acetogens use the A- and C-clusters of CODH/ACS to produce acetate from CO2, methanogens use A- and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO2 and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.
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Affiliation(s)
- Alison Biester
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Andrea N. Marcano-Delgado
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States,Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Bio-inspired
Solar Energy Program, Canadian Institute
for Advanced Research, Toronto, ON M5G 1M1, Canada,
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9
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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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10
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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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11
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Schaupp S, Arriaza-Gallardo FJ, Pan HJ, Kahnt J, Angelidou G, Paczia N, Costa K, Hu X, Shima S. In Vitro Biosynthesis of the [Fe]-Hydrogenase Cofactor Verifies the Proposed Biosynthetic Precursors. Angew Chem Int Ed Engl 2022; 61:e202200994. [PMID: 35286742 PMCID: PMC9314073 DOI: 10.1002/anie.202200994] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Indexed: 02/06/2023]
Abstract
In the FeGP cofactor of [Fe]‐hydrogenase, low‐spin FeII is in complex with two CO ligands and a pyridinol derivative; the latter ligates the iron with a 6‐acylmethyl substituent and the pyridinol nitrogen. A guanylylpyridinol derivative, 6‐carboxymethyl‐3,5‐dimethyl‐4‐guanylyl‐2‐pyridinol (3), is produced by the decomposition of the FeGP cofactor under irradiation with UV‐A/blue light and is also postulated to be a precursor of FeGP cofactor biosynthesis. HcgC and HcgB catalyze consecutive biosynthesis steps leading to 3. Here, we report an in vitro biosynthesis assay of the FeGP cofactor using the cell extract of the ΔhcgBΔhcgC strain of Methanococcus maripaludis, which does not biosynthesize 3. We chemically synthesized pyridinol precursors 1 and 2, and detected the production of the FeGP cofactor from 1, 2 and 3. These results indicated that 1, 2 and 3 are the precursors of the FeGP cofactor, and the carboxy group of 3 is converted to the acyl ligand.
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Affiliation(s)
- Sebastian Schaupp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | | | - Hui-Jie Pan
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Georgia Angelidou
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Kyle Costa
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, MN, USA
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
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12
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Biester A, Dementin S, Drennan CL. Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase. J Inorg Biochem 2022; 230:111774. [PMID: 35278753 PMCID: PMC9093221 DOI: 10.1016/j.jinorgbio.2022.111774] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/31/2022] [Accepted: 02/19/2022] [Indexed: 10/31/2022]
Abstract
Carbon monoxide dehydrogenase (CODH) plays an important role in the processing of the one‑carbon gases carbon monoxide and carbon dioxide. In CODH enzymes, these gases are channeled to and from the Ni-Fe-S active sites using hydrophobic cavities. In this work, we investigate these gas channels in a monofunctional CODH from Desulfovibrio vulgaris, which is unusual among CODHs for its oxygen-tolerance. By pressurizing D. vulgaris CODH protein crystals with xenon and solving the structure to 2.10 Å resolution, we identify 12 xenon sites per CODH monomer, thereby elucidating hydrophobic gas channels. We find that D. vulgaris CODH has one gas channel that has not been experimentally validated previously in a CODH, and a second channel that is shared with Moorella thermoacetica carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS). This experimental visualization of D. vulgaris CODH gas channels lays groundwork for further exploration of factors contributing to oxygen-tolerance in this CODH, as well as study of channels in other CODHs. We dedicate this publication to the memory of Dick Holm, whose early studies of the Ni-Fe-S clusters of CODH inspired us all.
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Affiliation(s)
- Alison Biester
- Dept. of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Sébastien Dementin
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Catherine L Drennan
- Dept. of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Dept. of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Canadian Institute for Advanced Research, Bio-inspired Solar Energy Program, Toronto, ON M5G 1M1, Canada.
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13
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Jeoung JH, Fesseler J, Domnik L, Klemke F, Sinnreich M, Teutloff C, Dobbek H. A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold. Angew Chem Int Ed Engl 2022; 61:e202117000. [PMID: 35133707 PMCID: PMC9311411 DOI: 10.1002/anie.202117000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Indexed: 11/12/2022]
Abstract
Ni,Fe‐containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO2 to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe‐cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS‐VCh. Its structure reveals the typical CODH scaffold, but contains an iron‐sulfur‐oxo hybrid‐cluster. Although closely related to true CODHs, CooS‐VCh catalyzes neither CO oxidation, nor CO2 reduction. The active site of CooS‐VCh undergoes a redox‐dependent restructuring between a reduced [4Fe‐3S]‐cluster and an oxidized [4Fe‐2S‐S*‐2O‐2(H2O)]‐cluster. Hydroxylamine, a slow‐turnover substrate of CooS‐VCh, oxidizes the hybrid‐cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O‐cluster in place of the Ni,Fe‐heterocubane‐cluster of CODHs.
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Affiliation(s)
- Jae-Hun Jeoung
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Jochen Fesseler
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Lilith Domnik
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Friederike Klemke
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Malte Sinnreich
- Freie Universität Berlin, Fachbereich Physik, Arnimallee 14, 14195, Berlin, Germany
| | - Christian Teutloff
- Freie Universität Berlin, Fachbereich Physik, Arnimallee 14, 14195, Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
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14
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Schaupp S, Arriaza‐Gallardo FJ, Pan H, Kahnt J, Angelidou G, Paczia N, Costa K, Hu X, Shima S. In Vitro Biosynthesis of the [Fe]‐Hydrogenase Cofactor Verifies the Proposed Biosynthetic Precursors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Schaupp
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | | | - Hui‐jie Pan
- Laboratory of Inorganic Synthesis and Catalysis Institute of Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305 1015 Lausanne Switzerland
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Georgia Angelidou
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Kyle Costa
- Department of Plant and Microbial Biology University of Minnesota Twin Cities St. Paul, MN USA
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis Institute of Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305 1015 Lausanne Switzerland
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
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15
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Jeoung J, Fesseler J, Domnik L, Klemke F, Sinnreich M, Teutloff C, Dobbek H. Ein sich umstrukturierender [4Fe‐3S‐nO]‐Cluster in einem Kohlenmonoxid‐Dehydrogenase‐Gerüst. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jae‐Hun Jeoung
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Jochen Fesseler
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Lilith Domnik
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Friederike Klemke
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Malte Sinnreich
- Freie Universität Berlin, Fachbereich Physik Arnimallee 14 14195 Berlin Deutschland
| | - Christian Teutloff
- Freie Universität Berlin, Fachbereich Physik Arnimallee 14 14195 Berlin Deutschland
| | - Holger Dobbek
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
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16
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Inoue M, Omae K, Nakamoto I, Kamikawa R, Yoshida T, Sako Y. Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases. Extremophiles 2022; 26:9. [PMID: 35059858 PMCID: PMC8776680 DOI: 10.1007/s00792-022-01259-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
Abstract
Ni-containing carbon monoxide dehydrogenase (Ni-CODH) plays an important role in the CO/CO2-based carbon and energy metabolism of microbiomes. Ni-CODH is classified into distinct phylogenetic clades, A–G, with possibly distinct cellular roles. However, the types of Ni-CODH clade used by organisms in different microbiomes are unknown. Here, we conducted a metagenomic survey of a protein database to determine the relationship between the phylogeny and biome distribution of Ni-CODHs. Clustering and phylogenetic analyses showed that the metagenome assembly-derived Ni-CODH sequences were distributed in ~ 60% Ni-CODH clusters and in all Ni-CODH clades. We also identified a novel Ni-CODH clade, clade H. Biome mapping on the Ni-CODH phylogenetic tree revealed that Ni-CODHs of almost all the clades were found in natural aquatic environmental and engineered samples, whereas those of specific subclades were found only in host-associated samples. These results are comparable with our finding that the diversity in the phylum-level taxonomy of host-associated Ni-CODH owners is statistically different from those of the other biomes. Our findings suggest that while Ni-CODH is a ubiquitous enzyme produced across diverse microbiomes, its distribution in each clade is biased and mainly affected by the distinct composition of microbiomes.
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Affiliation(s)
- Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
- R-GIRO, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Kimiho Omae
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Issei Nakamoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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17
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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18
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OUP accepted manuscript. Metallomics 2022; 14:6549566. [DOI: 10.1093/mtomcs/mfac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/02/2022] [Indexed: 11/12/2022]
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19
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Lee K, Choi J, Graham PM, Lee Y. Binding of carbon monoxide at a single nickel center and its oxidative reactivity toward
CO
2
and
O
2. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kunwoo Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Jonghoon Choi
- Department of Chemistry Seoul National University Seoul South Korea
| | - Peter M. Graham
- Department of Chemistry Saint Joseph's University Philadelphia Pennsylvania USA
| | - Yunho Lee
- Department of Chemistry Seoul National University Seoul South Korea
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20
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Terranova U. Residues surrounding the active centre of carbon monoxide dehydrogenase are key in converting [Formula: see text] to CO. J Biol Inorg Chem 2021; 26:617-624. [PMID: 34255144 DOI: 10.1007/s00775-021-01878-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/17/2021] [Indexed: 10/20/2022]
Abstract
The enzyme carbon monoxide dehydrogenase is capable of efficiently converting [Formula: see text] to CO and, therefore, can enable an affordable [Formula: see text] recycling strategy. The reduction of [Formula: see text] occurs at a peculiar nickel-iron-sulfur cluster, following a mechanism that remains little understood. In this study, we have used ab initio molecular dynamics simulations to explore the free energy landscape of the reaction. We predict the existence of a COOH ligand that strongly interacts with the surrounding protein residues and favours a mechanism where a [Formula: see text] molecule is eliminated before CO. We have taken advantages of the insights offered by our simulations to revisit the catalytic mechanism and the role of the residues surrounding the active centre in particular, thus assisting in the design of inorganic catalysts that mimic the enzyme.
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Affiliation(s)
- Umberto Terranova
- Faculty of Medicine and Health Sciences, Crewe Campus, University of Buckingham, Crewe, CW1 5DU, UK.
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21
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Fujishiro T, Ooi M, Takaoka K. Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion. FEBS J 2021; 288:6752-6768. [PMID: 34101368 DOI: 10.1111/febs.16062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 06/07/2021] [Indexed: 01/26/2023]
Abstract
Hybrid cluster protein (HCP) is a unique Fe-S-O-type metallocluster-containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X-ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Surprisingly, Ec HCP was found to harbor a [4Fe-4S] cluster rather than a [2Fe-2S] cluster at the N-terminal Cys-rich region, similar to class I HCPs. It was also found that the Cys-rich motif forms a unique protrusion and that the surrounding charge distributions on the surface of class II Ec HCP are distinct from those of class I HCPs. The functional significance of the Cys-rich region was investigated using an Ec HCP variant (chimeric HCP) containing a class I HCP Cys-rich motif from Desulfovibrio desulfuricans. The biochemical analyses showed that the chimeric HCP lacks the hybrid cluster and the electron-accepting function from HCR despite the formation of the chimeric HCP-HCR complex. Furthermore, HCP-HCR molecular docking analysis suggested that the protrusion area serves as an HCR-binding region. Therefore, the protrusion of the unique Cys-rich motif and the surrounding area of class II HCP are likely important for maturation of Ec HCP and orienting HCR onto the surface of HCP to facilitate electron transfer in the HCP-HCR complex.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miho Ooi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kyosei Takaoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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22
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Lemaire ON, Wagner T. Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148330. [PMID: 33080205 DOI: 10.1016/j.bbabio.2020.148330] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/01/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
Clostridium autoethanogenum, the bacterial model for biological conversion of waste gases into biofuels, grows under extreme carbon-monoxide (CO) concentrations. The strictly anaerobic bacterium derives its entire cellular energy and carbon from this poisonous gas, therefore requiring efficient molecular machineries for CO-conversion. Here, we structurally and biochemically characterized the key enzyme of the CO-converting metabolism: the CO-dehydrogenase/Acetyl-CoA synthase (CODH/ACS). We obtained crystal structures of natively isolated complexes from fructose-grown and CO-grown C. autoethanogenum cultures. Both contain the same isoforms and if the overall structure adopts the classic α2β2 architecture, comparable to the model enzyme from Moorella thermoacetica, the ACS binds a different position on the CODH core. The structural characterization of a proteolyzed complex and the conservation of the binding interface in close homologs rejected the possibility of a crystallization artefact. Therefore, the internal CO-channeling system, critical to transfer CO generated at the C-cluster to the ACS active site, drastically differs in the complex from C. autoethanogenum. The 1.9-Å structure of the CODH alone provides an accurate picture of the new CO-routes, leading to the ACS core and reaching the surface. Increased gas accessibility would allow the simultaneous CO-oxidation and acetyl-CoA production. Biochemical experiments showed higher flexibility of the ACS subunit from C. autoethanogenum compared to M. thermoacetica, albeit monitoring similar CO-oxidation and formation rates. These results show a reshuffling of internal CO-tunnels during evolution of these Firmicutes, putatively leading to a bidirectional complex that ensure a high flux of CO-conversion toward energy conservation, acting as the main cellular powerplant.
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Affiliation(s)
- Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany.
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23
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Prat JR, Gaggioli CA, Cammarota RC, Bill E, Gagliardi L, Lu CC. Bioinspired Nickel Complexes Supported by an Iron Metalloligand. Inorg Chem 2020; 59:14251-14262. [PMID: 32954721 DOI: 10.1021/acs.inorgchem.0c02041] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nature utilizes multimetallic sites in metalloenzymes to enable multielectron chemical transformations at ambient conditions and low overpotentials. One such example of multimetallic cooperativity can be found in the C-cluster of Ni-carbon monoxide dehydrogenase (CODH), which interconverts CO and CO2. Toward a potential functional model of the C-cluster, a family of Ni-Fe bimetallic complexes was synthesized that contain direct metal-metal bonding interactions. The complexes were characterized by X-ray crystallography, various spectroscopies (NMR, EPR, UV-vis, Mössbauer), and theoretical calculations. The Ni-Fe bimetallic system has a reversible Fe(III)/Fe(II) redox couple at -2.10 V (vs Fc+/Fc). The Fe-based "redox switch" can turn on CO2 reactivity at the Ni(0) center by leveraging the Ni→Fe dative interaction to attenuate the Ni(0) electron density. The reduced Ni(0)Fe(II) species mediated the formal two-electron reduction of CO2 to CO, providing a Ni-CO adduct and CO32- as products. During the reaction, an intermediate was observed that is proposed to be a Ni-CO2 species.
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Affiliation(s)
| | | | | | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
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24
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Ferry JG. Methanosarcina acetivorans: A Model for Mechanistic Understanding of Aceticlastic and Reverse Methanogenesis. Front Microbiol 2020; 11:1806. [PMID: 32849414 PMCID: PMC7399021 DOI: 10.3389/fmicb.2020.01806] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/09/2020] [Indexed: 11/13/2022] Open
Abstract
Acetate-utilizing methanogens are responsible for approximately two-thirds of the one billion metric tons of methane produced annually in Earth's anaerobic environments. Methanosarcina acetivorans has emerged as a model organism for the mechanistic understanding of aceticlastic methanogenesis and reverse methanogenesis applicable to understanding the methane and carbon cycles in nature. It has the largest genome in the Archaea, supporting a metabolic complexity that enables a remarkable ability for adapting to environmental opportunities and challenges. Biochemical investigations have revealed an aceticlastic pathway capable of fermentative and respiratory energy conservation that explains how Ms. acetivorans is able to grow and compete in the environment. The mechanism of respiratory energy conservation also plays a role in overcoming endothermic reactions that are key to reversing methanogenesis.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
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25
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Isegawa M, Matsumoto T, Ogo S. Selective Oxidation of H 2 and CO by NiIr Catalyst in Aqueous Solution: A DFT Mechanistic Study. Inorg Chem 2020; 59:1014-1028. [PMID: 31898897 DOI: 10.1021/acs.inorgchem.9b02400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the challenges in utilizing hydrogen gas (H2) as a sustainable fossil fuel alternative is the inhibition of H2 oxidation by carbon monoxide (CO), which is involved in the industrial production of H2 sources. To solve this problem, a catalyst that selectively oxidizes either CO or H2 or one that co-oxidizes H2 and CO is needed. Recently, a NiIr catalyst [NiIICl(X)IrIIICl(η5-C5Me5)], (X = N,N'-dimethyl-3,7-diazanonane-1,9-dithiolate), which efficiently and selectively oxidizes either H2 or CO depending on the pH, has been developed (Angew. Chem. Int. Ed. 2017, 56, 9723-9726). In the present work, density functional theory (DFT) calculations are employed to elucidate the pH-dependent reaction mechanisms of H2 and CO oxidation catalyzed by this NiIr catalyst. During H2 oxidation, our calculations suggest that dihydrogen binds to the Ir center and generates an Ir(III)-dihydrogen complex, followed by subsequent isomerization to an Ir(V)-dihydride species. Then, a proton is abstracted by a buffer base, CH3COO-, resulting in the formation of a hydride complex. The catalytic cycle completes with electron transfer from the hydride complex to a protonated 2,6-dichlorobenzeneindophenol (DCIP) and a proton transfer from the oxidized hydride complex to a buffer base. The CO oxidation mechanism involves three distinct steps, i.e., (1) formation of a metal carbonyl complex, (2) formation of a metallocarboxylic acid, and (3) conversion of the metallocarboxylic acid to a hydride complex. The formation of the metallocarboxylic acid involves nucleophilic attack of OH- to the carbonyl-C followed by a large structural change with concomitant cleavage of the Ir-S bond and rotation of the COOH group along the NiIr axis. During the conversion of the metallocarboxylic acid to the hydride complex, intramolecular proton transfer followed by removal of CO2 leads to the formation of the hydride complexes. In addition, the barrier heights for the binding of small molecules (H2, OH-, H2O, and CO) to Ir were calculated, and the results indicated that dissociation from Ir is a faster process than the binding of H2O and H2. These calculations indicate that H2 oxidation is inhibited by CO and OH- and thus prefers acidic conditions. In contrast, the CO oxidation reactions occur more favorably under basic conditions, as the formation of the metallocarboxylic acid involves OH- attack to a carbonyl-C and the binding of OH- to Ni largely stabilizes the triplet spin state of the complex. Taken together, these calculations provide a rationale for the experimentally observed pH-dependent, selective oxidations of H2 and CO.
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Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , 744 Moto-oka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , 744 Moto-oka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , 744 Moto-oka , Nishi-ku, Fukuoka 819-0395 , Japan
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26
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Fukuyama Y, Inoue M, Omae K, Yoshida T, Sako Y. Anaerobic and hydrogenogenic carbon monoxide-oxidizing prokaryotes: Versatile microbial conversion of a toxic gas into an available energy. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:99-148. [PMID: 32386607 DOI: 10.1016/bs.aambs.2019.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbon monoxide (CO) is a gas that is toxic to various organisms including humans and even microbes; however, it has low redox potential, which can fuel certain microbes, namely, CO oxidizers. Hydrogenogenic CO oxidizers utilize an energy conservation system via a CO dehydrogenase/energy-converting hydrogenase complex to produce hydrogen gas, a zero emission fuel, by CO oxidation coupled with proton reduction. Biochemical and molecular biological studies using a few model organisms have revealed their enzymatic reactions and transcriptional response mechanisms using CO. Biotechnological studies for CO-dependent hydrogen production have also been carried out with these model organisms. In this chapter, we review recent advances in the studies of these microbes, which reveal their unique and versatile metabolic profiles and provides future perspectives on ecological roles and biotechnological applications. Over the past decade, the number of isolates has doubled (37 isolates in 5 phyla, 20 genera, and 32 species). Some of the recently isolated ones show broad specificity to electron acceptors. Moreover, accumulating genomic information predicts their unique physiologies and reveals their phylogenomic relationships with novel potential hydrogenogenic CO oxidizers. Combined with genomic database surveys, a molecular ecological study has unveiled the wide distribution and low abundance of these microbes. Finally, recent biotechnological applications of hydrogenogenic CO oxidizers have been achieved via diverse approaches (e.g., metabolic engineering and co-cultivation), and the identification of thermophilic facultative anaerobic CO oxidizers will promote industrial applications as oxygen-tolerant biocatalysts for efficient hydrogen production by genomic engineering.
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Affiliation(s)
- Yuto Fukuyama
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masao Inoue
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kimiho Omae
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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27
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Liao RZ, Siegbahn PEM. Energetics for the Mechanism of Nickel-Containing Carbon Monoxide Dehydrogenase. Inorg Chem 2019; 58:7931-7938. [PMID: 31141352 DOI: 10.1021/acs.inorgchem.9b00644] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nickel-containing carbon monoxide (CO) dehydrogenase is an enzyme that catalyzes the important reversible carbon dioxide reduction. Several high-resolution structures have been determined at various stages of the reduction, which can be used as good starting points for the present computational study. The cluster model is used in combination with a systematic application of the density functional theory as recently described. The results are in very good agreement with experimental evidence. There are a few important results. To explain why the X-ray structure for the reduced Cred1 state has an empty site on nickel, it is here suggested that the cluster has been over-reduced by X-rays and is therefore not the desired reduced state, which instead contains a bound CO on nickel. After an additional reduction, a hydride bound to nickel is suggested to play a role. In order to obtain energetics in agreement with experiments, it is concluded that one sulfide bridge in the Ni-Fe cluster should be protonated. The best test of the accuracy obtained is to compare the computed rate for reduction using -0.6 V with that for oxidation using -0.3 V, where good agreement was obtained. Obtaining a mechanism that is easily reversible is another demanding aspect of the modeling. Nickel oscillates between nickel(II) and nickel(I), while nickel(0) never comes in.
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Affiliation(s)
- Rong-Zhen Liao
- Key Laboratory for Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Media, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , Wuhan 430074 , China
| | - Per E M Siegbahn
- Arrhenius Laboratory, Department of Organic Chemistry , Stockholm University , Stockholm SE-10691 , Sweden
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28
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Inoue M, Nakamoto I, Omae K, Oguro T, Ogata H, Yoshida T, Sako Y. Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases. Front Microbiol 2019; 9:3353. [PMID: 30705673 PMCID: PMC6344411 DOI: 10.3389/fmicb.2018.03353] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/31/2018] [Indexed: 11/30/2022] Open
Abstract
Anaerobic Ni-containing carbon-monoxide dehydrogenases (Ni-CODHs) catalyze the reversible conversion between carbon monoxide and carbon dioxide as multi-enzyme complexes responsible for carbon fixation and energy conservation in anaerobic microbes. However, few biochemically characterized model enzymes exist, with most Ni-CODHs remaining functionally unknown. Here, we performed phylogenetic and structure-based Ni-CODH classification using an expanded dataset comprised of 1942 non-redundant Ni-CODHs from 1375 Ni-CODH-encoding genomes across 36 phyla. Ni-CODHs were divided into seven clades, including a novel clade. Further classification into 24 structural groups based on sequence analysis combined with structural prediction revealed diverse structural motifs for metal cluster formation and catalysis, including novel structural motifs potentially capable of forming metal clusters or binding metal ions, indicating Ni-CODH diversity and plasticity. Phylogenetic analysis illustrated that the metal clusters responsible for intermolecular electron transfer were drastically altered during evolution. Additionally, we identified novel putative Ni-CODH-associated proteins from genomic contexts other than the Wood–Ljungdahl pathway and energy converting hydrogenase system proteins. Network analysis among the structural groups of Ni-CODHs, their associated proteins and taxonomies revealed previously unrecognized gene clusters for Ni-CODHs, including uncharacterized structural groups with putative metal transporters, oxidoreductases, or transcription factors. These results suggested diversification of Ni-CODH structures adapting to their associated proteins across microbial genomes.
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Affiliation(s)
- Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Issei Nakamoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kimiho Omae
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tatsuki Oguro
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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29
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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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30
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Xavier JC, Preiner M, Martin WF. Something special about CO-dependent CO 2 fixation. FEBS J 2018; 285:4181-4195. [PMID: 30240136 PMCID: PMC6282760 DOI: 10.1111/febs.14664] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/08/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023]
Abstract
Carbon dioxide enters metabolism via six known CO2 fixation pathways, of which only one is linear, exergonic in the direction of CO2‐assimilation, and present in both bacterial and archaeal anaerobes – the Wood‐Ljungdahl (WL) or reductive acetyl‐CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO2. We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO2, which are non‐randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO2, only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni‐ and Fe‐containing enzyme that generates CO for CO2 fixation in the WL pathway, and aerobic CODH, a Mo‐ and Cu‐containing enzyme that oxidizes environmental CO as an electron source. The CO‐dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon‐nickel at the Ni‐Fe‐S A‐cluster of acetyl‐CoA synthase (ACS). It appears that no alternative mechanisms to the CO‐dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism.
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Affiliation(s)
- Joana C Xavier
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - Martina Preiner
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - William F Martin
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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31
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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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32
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Yazdanpanah A, Ghasimi DSM, Kim MG, Nakhla G, Hafez H, Keleman M. Impact of trace element supplementation on mesophilic anaerobic digestion of food waste using Fe-rich inoculum. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29240-29255. [PMID: 30117028 DOI: 10.1007/s11356-018-2832-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Trace elements (TEs) play an indispensable role in enhancing the stability of anaerobic digestion (AD) of food waste (FW). Significant research on AD of FW with TE supplementation has been conducted with low Fe content inoculum. However, the use of Fe-rich inoculum is inevitable due to chemical phosphorous removal from wastewater in North America. We conducted comprehensive mesophilic batch tests to investigate the effect of TEs (Fe, Ni, Co, Se, and Mo) on FW digestion inoculated with Fe-rich sludge (≥ 1000 mg Fe L-1). This paper presents the impact of supplementing various concentrations of TEs on specific methanogenic activity (SMA), maximum specific methane production rate (SMPRmax), and apparent hydrolysis rate constant (Kh). The addition of TEs adversely impacted methanogenic activity by 20 to 58% in the SMA tests. The effects of individual and mixed supplementation of TEs on the SMPRmax and Kh during FW digestion were negligible; exceptions include Fe, Mo, and Co. Final soluble TE concentrations were 10-29% of the initial soluble TEs. The high Fe concentration in the inoculum reduces the bioavailable fraction of added TEs via coprecipitation. Contrary with many literature reports indicating the need to supplement TE to improve FW digestion efficiency, with Fe-rich sludges, FW digestion does not require TE supplementation.
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Affiliation(s)
- Andisheh Yazdanpanah
- Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Western Ontario, London, ON, Canada
| | | | - Min Gu Kim
- Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Western Ontario, London, ON, Canada
| | - George Nakhla
- Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Western Ontario, London, ON, Canada.
| | - Hisham Hafez
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Western Ontario, London, ON, Canada
| | - Michele Keleman
- Emerson Electric Co., 8000 West Florissant Ave., St. Louis, MO, USA
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33
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Biomimetic Approach to CO 2 Reduction. Bioinorg Chem Appl 2018; 2018:2379141. [PMID: 30154831 PMCID: PMC6093055 DOI: 10.1155/2018/2379141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/26/2018] [Accepted: 07/04/2018] [Indexed: 01/14/2023] Open
Abstract
The development of artificial photosynthetic technologies able to produce solar-fuels from CO2 reduction is a fundamental task that requires the employment of specific catalysts being accomplished. Besides, effective catalysts are also demanded to capture atmospheric CO2, mitigating the effects of its constantly increasing emission. Biomimetic transition metal complexes are considered ideal platforms to develop efficient and selective catalysts to be implemented in electrocatalytic and photocatalytic devices. These catalysts, designed according to the inspiration provided by nature, are simple synthetic molecular systems capable of mimic features of the enzymatic activity. The present review aims to focus the attention on the mechanistic and structural aspects highlighted to be necessary to promote a proper catalytic activity. The determination of these characteristics is of interest both for clarifying aspects of the catalytic cycle of natural enzymes that are still unknown and for developing synthetic molecular catalysts that can readily be applied to artificial photosynthetic devices.
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34
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Zhang N, Peng H, Li Y, Yang W, Zou Y, Duan H. Ammonia determines transcriptional profile of microorganisms in anaerobic digestion. Braz J Microbiol 2018; 49:770-776. [PMID: 29937264 PMCID: PMC6175727 DOI: 10.1016/j.bjm.2018.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 02/27/2018] [Accepted: 04/13/2018] [Indexed: 01/13/2023] Open
Abstract
Anaerobic digestion is important for the management of livestock manure with high ammonia level. Although ammonia effects on anaerobic digestion have been comprehensively studied, the molecular mechanism underlying ammonia inhibition still remains elusive. In this study, based on metatranscriptomic analysis, the transcriptional profile of microbial community in anaerobic digestion under low (1500 mg L−1) and high NH4+ (5000 mg L−1) concentrations, respectively, were revealed. The results showed that high NH4+ concentrations significantly inhibited methane production but facilitated the accumulations of volatile fatty acids. The expression of methanogenic pathway was significantly inhibited by high NH4+ concentration but most of the other pathways were not significantly affected. Furthermore, the expressions of methanogenic genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase were significantly inhibited by high NH4+ concentration. The inhibition of the co-expressions of the genes which encode acetyl-CoA decarbonylase was observed. Some genes involved in the pathways of aminoacyl-tRNA biosynthesis and ribosome were highly expressed under high NH4+ concentration. Consequently, the ammonia inhibition on anaerobic digestion mainly focused on methanogenic process by suppressing the expressions of genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase. This study improved the accuracy and depth of understanding ammonia inhibition on anaerobic digestion.
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Affiliation(s)
- Nan Zhang
- Neijiang Normal University, College of Life Sciences, Neijiang, China; Department of Education, Key Laboratory of Regional Characteristic Agricultural Resources, Neijiang, China
| | - Huijuan Peng
- Neijiang Normal University, College of Life Sciences, Neijiang, China; Department of Education, Key Laboratory of Regional Characteristic Agricultural Resources, Neijiang, China
| | - Yong Li
- Neijiang Normal University, College of Life Sciences, Neijiang, China; Department of Education, Key Laboratory of Regional Characteristic Agricultural Resources, Neijiang, China
| | - Wenxiu Yang
- Neijiang Normal University, College of Life Sciences, Neijiang, China
| | - Yuneng Zou
- Neijiang Normal University, College of Life Sciences, Neijiang, China
| | - Huiguo Duan
- Neijiang Normal University, College of Life Sciences, Neijiang, China.
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35
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Photosynthetic water splitting by the Mn4Ca2+OX catalyst of photosystem II: its structure, robustness and mechanism. Q Rev Biophys 2018; 50:e13. [PMID: 29233225 DOI: 10.1017/s0033583517000105] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The biological energy cycle of our planet is driven by photosynthesis whereby sunlight is absorbed by chlorophyll and other accessory pigments. The excitation energy is then efficiently transferred to a reaction centre where charge separation occurs in a few picoseconds. In the case of photosystem II (PSII), the energy of the charge transfer state is used to split water into oxygen and reducing equivalents. This is accomplished by the relatively low energy content of four photons of visible light. PSII is a large multi-subunit membrane protein complex embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Four high energy electrons, together with four protons (4H+), are used to reduce plastoquinone (PQ), the terminal electron acceptor of PSII, to plastoquinol (PQH2). PQH2 passes its reducing equivalents to an electron transfer chain which feeds into photosystem I (PSI) where they gain additional reducing potential from a second light reaction which is necessary to drive CO2 reduction. The catalytic centre of PSII consists of a cluster of four Mn ions and a Ca2+ linked by oxo bonds. In addition, there are seven amino acid ligands. In this Article, I discuss the structure of this metal cluster, its stability and the probability that an acid-base (nucleophilic-electrophilic) mechanism catalyses the water splitting reaction on the surface of the metal-cluster. Evidence for this mechanism is presented from studies on water splitting catalysts consisting of organo-complexes of ruthenium and manganese and also by comparison with the enzymology of carbon monoxide dehydrogenase (CODH). Finally the relevance of our understanding of PSII is discussed in terms of artificial photosynthesis with emphasis on inorganic water splitting catalysts as oxygen generating photoelectrodes.
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36
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Nichols EM, Derrick JS, Nistanaki SK, Smith PT, Chang CJ. Positional effects of second-sphere amide pendants on electrochemical CO 2 reduction catalyzed by iron porphyrins. Chem Sci 2018; 9:2952-2960. [PMID: 29732079 PMCID: PMC5915798 DOI: 10.1039/c7sc04682k] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/14/2018] [Indexed: 12/22/2022] Open
Abstract
The development of catalysts for electrochemical reduction of carbon dioxide offers an attractive approach to transforming this greenhouse gas into value-added carbon products with sustainable energy input. Inspired by natural bioinorganic systems that feature precisely positioned hydrogen-bond donors in the secondary coordination sphere to direct chemical transformations occurring at redox-active metal centers, we now report the design, synthesis, and characterization of a series of iron tetraphenylporphyrin (Fe-TPP) derivatives bearing amide pendants at various positions at the periphery of the metal core. Proper positioning of the amide pendants greatly affects the electrocatalytic activity for carbon dioxide reduction to carbon monoxide. In particular, derivatives bearing proximal and distal amide pendants on the ortho position of the phenyl ring exhibit significantly larger turnover frequencies (TOF) compared to the analogous para-functionalized amide isomers or unfunctionalized Fe-TPP. Analysis of TOF as a function of catalyst standard reduction potential enables first-sphere electronic effects to be disentangled from second-sphere through-space interactions, suggesting that the ortho-functionalized porphyrins can utilize the latter second-sphere property to promote CO2 reduction. Indeed, the distally-functionalized ortho-amide isomer shows a significantly larger through-space interaction than its proximal ortho-amide analogue. These data establish that proper positioning of secondary coordination sphere groups is an effective design element for breaking electronic scaling relationships that are often observed in electrochemical CO2 reduction.
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Affiliation(s)
- Eva M Nichols
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
| | - Jeffrey S Derrick
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
| | - Sepand K Nistanaki
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
| | - Peter T Smith
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
| | - Christopher J Chang
- Department of Chemistry , University of California , Berkeley , CA 94720 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
- Department of Molecular and Cell Biology , University of California , Berkeley , CA 94720 , USA
- Howard Hughes Medical Institute , University of California , Berkeley , CA 94720 , USA
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37
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Adam PS, Borrel G, Gribaldo S. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Proc Natl Acad Sci U S A 2018; 115:E1166-E1173. [PMID: 29358391 PMCID: PMC5819426 DOI: 10.1073/pnas.1716667115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of uncultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
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Affiliation(s)
- Panagiotis S Adam
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Guillaume Borrel
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Simonetta Gribaldo
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France;
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38
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Sahoo D, Yoo C, Lee Y. Direct CO 2 Addition to a Ni(0)-CO Species Allows the Selective Generation of a Nickel(II) Carboxylate with Expulsion of CO. J Am Chem Soc 2018; 140:2179-2185. [PMID: 29343060 DOI: 10.1021/jacs.7b11074] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Addition of CO2 to a low-valent nickel species has been explored with a newly designed acriPNP pincer ligand (acriPNP- = 4,5-bis(diisopropylphosphino)-2,7,9,9-tetramethyl-9H-acridin-10-ide). This is a crucial step in understanding biological CO2 conversion to CO found in carbon monoxide dehydrogenase (CODH). A four-coordinate nickel(0) state was reliably accessed in the presence of a CO ligand, which can be prepared from a stepwise reduction of a cationic {(acriPNP)Ni(II)-CO}+ species. All three Ni(II), Ni(I), and Ni(0) monocarbonyl species were cleanly isolated and spectroscopically characterized. Addition of electrons to the nickel(II) species significantly alters its geometry from square planar toward tetrahedral because of the filling of the dx2-y2 orbital. Accordingly, the CO ligand position changes from equatorial to axial, ∠N-Ni-C of 176.2(2)° to 129.1(4)°, allowing opening of a CO2 binding site. Upon addition of CO2 to a nickel(0)-CO species, a nickel(II) carboxylate species with a Ni(η1-CO2-κC) moiety was formed and isolated (75%). This reaction occurs with the concomitant expulsion of CO(g). This is a unique result markedly different from our previous report involving the flexible analogous PNP ligand, which revealed the formation of multiple products including a tetrameric cluster from the reaction with CO2. Finally, the carbon dioxide conversion to CO at a single nickel center is modeled by the successful isolation of all relevant intermediates, such as Ni-CO2, Ni-COOH, and Ni-CO.
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Affiliation(s)
- Dipankar Sahoo
- Department of Chemistry, Korea Advanced Institute of Science and Technology , Daejeon 34141, Republic of Korea
| | - Changho Yoo
- Department of Chemistry, Korea Advanced Institute of Science and Technology , Daejeon 34141, Republic of Korea
| | - Yunho Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology , Daejeon 34141, Republic of Korea
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39
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Kwawu CR, Tia R, Adei E, Dzade NY, Catlow CRA, de Leeuw NH. CO 2 activation and dissociation on the low miller index surfaces of pure and Ni-coated iron metal: a DFT study. Phys Chem Chem Phys 2018; 19:19478-19486. [PMID: 28718470 DOI: 10.1039/c7cp03466k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have used spin polarized density functional theory calculations to perform extensive mechanistic studies of CO2 dissociation into CO and O on the clean Fe(100), (110) and (111) surfaces and on the same surfaces coated by a monolayer of nickel. CO2 chemisorbs on all three bare facets and binds more strongly to the stepped (111) surface than on the open flat (100) and close-packed (110) surfaces, with adsorption energies of -88.7 kJ mol-1, -70.8 kJ mol-1 and -116.8 kJ mol-1 on the (100), (110) and (111) facets, respectively. Compared to the bare Fe surfaces, we found weaker binding of the CO2 molecules on the Ni-deposited surfaces, where the adsorption energies are calculated at +47.2 kJ mol-1, -29.5 kJ mol-1 and -65.0 kJ mol-1 on the Ni-deposited (100), (110) and (111) facets respectively. We have also investigated the thermodynamics and activation energies for CO2 dissociation into CO and O on the bare and Ni-deposited surfaces. Generally, we found that the dissociative adsorption states are thermodynamically preferred over molecular adsorption, with the dissociation most favoured thermodynamically on the close-packed (110) facet. The trends in activation energy barriers were observed to follow that of the trends in surface work functions; consequently, the increased surface work functions observed on the Ni-deposited surfaces resulted in increased dissociation barriers and vice versa. These results suggest that measures to lower the surface work function will kinetically promote the dissociation of CO2 into CO and O, although the instability of the activated CO2 on the Ni-covered surfaces will probably result in CO2 desorption from the nickel-doped iron surfaces, as is also seen on the Fe(110) surface.
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Affiliation(s)
- Caroline R Kwawu
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard Tia
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Evans Adei
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Nelson Y Dzade
- Department of Earth Sciences, Utrecht University, Princetonplein 9, 3584 CC, Utrecht, The Netherlands.
| | - C Richard A Catlow
- School of Chemistry, Cardiff University, Main Building, Park PI, Cardiff CF10 3AT, UK.
| | - Nora H de Leeuw
- Department of Earth Sciences, Utrecht University, Princetonplein 9, 3584 CC, Utrecht, The Netherlands. and School of Chemistry, Cardiff University, Main Building, Park PI, Cardiff CF10 3AT, UK.
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40
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Different substrate regimes determine transcriptional profiles and gene co-expression in Methanosarcina barkeri (DSM 800). Appl Microbiol Biotechnol 2017; 101:7303-7316. [DOI: 10.1007/s00253-017-8457-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/26/2017] [Accepted: 07/30/2017] [Indexed: 01/15/2023]
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41
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Zhang A, Raje S, Liu J, Li X, Angamuthu R, Tung CH, Wang W. Nickel-Mediated Stepwise Transformation of CO to Acetaldehyde and Ethanol. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00472] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ailing Zhang
- School
of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Sakthi Raje
- Laboratory
of Inorganic Synthesis and Bioinspired Catalysis (LISBIC), Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jianguo Liu
- School
of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Xiaoyan Li
- School
of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Raja Angamuthu
- Laboratory
of Inorganic Synthesis and Bioinspired Catalysis (LISBIC), Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Chen-Ho Tung
- School
of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Wenguang Wang
- School
of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Jinan 250100, China
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42
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Barber J. A mechanism for water splitting and oxygen production in photosynthesis. NATURE PLANTS 2017; 3:17041. [PMID: 28368386 DOI: 10.1038/nplants.2017.41] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/03/2017] [Indexed: 05/26/2023]
Abstract
Sunlight is absorbed and converted to chemical energy by photosynthetic organisms. At the heart of this process is the most fundamental reaction on Earth, the light-driven splitting of water into its elemental constituents. In this way molecular oxygen is released, maintaining an aerobic atmosphere and creating the ozone layer. The hydrogen that is released is used to convert carbon dioxide into the organic molecules that constitute life and were the origin of fossil fuels. Oxidation of these organic molecules, either by respiration or combustion, leads to the recombination of the stored hydrogen with oxygen, releasing energy and reforming water. This water splitting is achieved by the enzyme photosystem II (PSII). Its appearance at least 3 billion years ago, and linkage through an electron transfer chain to photosystem I, directly led to the emergence of eukaryotic and multicellular organisms. Before this, biological organisms had been dependent on hydrogen/electron donors, such as H2S, NH3, organic acids and Fe2+, that were in limited supply compared with the oceans of liquid water. However, it is likely that water was also used as a hydrogen source before the emergence of PSII, as found today in anaerobic prokaryotic organisms that use carbon monoxide as an energy source to split water. The enzyme that catalyses this reaction is carbon monoxide dehydrogenase (CODH). Similarities between PSII and the iron- and nickel-containing form of this enzyme (Fe-Ni CODH) suggest a possible mechanism for the photosynthetic O-O bond formation.
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Affiliation(s)
- James Barber
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
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43
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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44
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Ciaccafava A, Tombolelli D, Domnik L, Fesseler J, Jeoung JH, Dobbek H, Mroginski MA, Zebger I, Hildebrandt P. When the inhibitor tells more than the substrate: the cyanide-bound state of a carbon monoxide dehydrogenase. Chem Sci 2016; 7:3162-3171. [PMID: 29997808 PMCID: PMC6005268 DOI: 10.1039/c5sc04554a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/27/2016] [Indexed: 11/21/2022] Open
Abstract
An integral approach including experimental and theoretical analysis has been carried out with the wild-type and engineered CODHIICh variant to assess the parameters that control the C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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N stretching frequency.
Carbon monoxide dehydrogenase (CODH) is a key enzyme for reversible CO interconversion. To elucidate structural and mechanistic details of CO binding at the CODH active site (C-cluster), cyanide is frequently used as an iso-electronic substitute and inhibitor. However, previous studies revealed conflicting results on the structure of the cyanide-bound complex and the mechanism of cyanide-inhibition. To address this issue in this work, we have employed IR spectroscopy, crystallography, site directed mutagenesis, and theoretical methods to analyse the cyanide complex of the CODH from Carboxydothermus hydrogenoformans (CODHIICh). IR spectroscopy demonstrates that a single cyanide binds to the Ni ion. Whereas the inhibitor could be partially removed at elevated temperature, irreversible degradation of the C-cluster occurred in the presence of an excess of cyanide on the long-minute time scale, eventually leading to the formation of [Fe(CN)6]4– and [Ni(CN)4]2– complexes. Theoretical calculations based on a new high-resolution structure of the cyanide-bound CODHIICh indicated that cyanide binding to the Ni ion occurs upon dissociation of the hydroxyl ligand from the Fe1 subsite of the C-cluster. The hydroxyl group is presumably protonated by Lys563 which, unlike to His93, does not form a hydrogen bond with the cyanide ligand. A stable deprotonated ε-amino group of Lys563 in the cyanide complex is consistent with the nearly unchanged C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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N stretching in the Lys563Ala variant of CODHIICh. These findings support the view that the proton channel connecting the solution phase with the active site displays a strict directionality, controlled by the oxidation state of the C-cluster.
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Affiliation(s)
- Alexandre Ciaccafava
- Technische Universität Berlin , Institut für Chemie , Sekretariat PC 14 , D-10623 Berlin , Germany . ; ;
| | - Daria Tombolelli
- Technische Universität Berlin , Institut für Chemie , Sekretariat PC 14 , D-10623 Berlin , Germany . ; ;
| | - Lilith Domnik
- Humboldt-Universität zu Berlin , Institut für Biologie , Unter den Linden 6 , D-10099 Berlin , Germany
| | - Jochen Fesseler
- Humboldt-Universität zu Berlin , Institut für Biologie , Unter den Linden 6 , D-10099 Berlin , Germany
| | - Jae-Hun Jeoung
- Humboldt-Universität zu Berlin , Institut für Biologie , Unter den Linden 6 , D-10099 Berlin , Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin , Institut für Biologie , Unter den Linden 6 , D-10099 Berlin , Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin , Institut für Chemie , Sekretariat PC 14 , D-10623 Berlin , Germany . ; ;
| | - Ingo Zebger
- Technische Universität Berlin , Institut für Chemie , Sekretariat PC 14 , D-10623 Berlin , Germany . ; ;
| | - Peter Hildebrandt
- Technische Universität Berlin , Institut für Chemie , Sekretariat PC 14 , D-10623 Berlin , Germany . ; ;
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Kumar P, Gupta R. The wonderful world of pyridine-2,6-dicarboxamide based scaffolds. Dalton Trans 2016; 45:18769-18783. [DOI: 10.1039/c6dt03578g] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This perspective focusses on a variety of scaffolds based on a pyridine-2,6-dicarboxamide fragment and their noteworthy roles in coordination chemistry, biomimetic studies, catalysis, and sensing.
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Affiliation(s)
- Pramod Kumar
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
| | - Rajeev Gupta
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
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Ferry JG. Acetate Metabolism in Anaerobes from the Domain Archaea. Life (Basel) 2015; 5:1454-71. [PMID: 26068860 PMCID: PMC4500148 DOI: 10.3390/life5021454] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/01/2015] [Indexed: 01/26/2023] Open
Abstract
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth's biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Majumdar A. Bioinorganic modeling chemistry of carbon monoxide dehydrogenases: description of model complexes, current status and possible future scopes. Dalton Trans 2015; 43:12135-45. [PMID: 24984248 DOI: 10.1039/c4dt00729h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Carbon monoxide dehydrogenases (CODHs) use CO as their sole source of carbon and energy and are found in both aerobic and anaerobic carboxidotrophic bacteria. Reversible transformation of CO to CO2 is catalyzed by a bimetallic [Mo-(μ2-S)-Cu] system in aerobic and by a highly asymmetric [Ni-Fe-S] cluster in anaerobic CODH active sites. The CODH activity in the microorganisms effects the removal of almost 10(8) tons of CO annually from the lower atmosphere and earth and thus help to maintain a sub-toxic concentration of CO. Despite an appreciable amount of work, the mechanism of CODH activity is not clearly understood yet. Moreover, biomimetic chemistry directed towards the active sites of CODHs faces several synthetic challenges. The synthetic problems associated with the modeling chemistry and strategies adopted to overcome those problems are discussed along with their limitations. A critical analysis of the exciting results delineating the present status of CODH modeling chemistry and its future prospects are presented.
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Affiliation(s)
- Amit Majumdar
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India.
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Scott A, Pelmenschikov V, Guo Y, Yan L, Wang H, George SJ, Dapper CH, Newton WE, Yoda Y, Tanaka Y, Cramer SP. Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom. J Am Chem Soc 2014; 136:15942-54. [PMID: 25275608 PMCID: PMC4235365 DOI: 10.1021/ja505720m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 01/21/2023]
Abstract
The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.
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Affiliation(s)
- Aubrey
D. Scott
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | | | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lifen Yan
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Hongxin Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Simon J. George
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Christie H. Dapper
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - William E. Newton
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - Yoshitaka Yoda
- Research
and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- SR
Materials Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Stephen P. Cramer
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
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50
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part II. {[Fe2S2](SγCys)4} proteins. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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