1
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Park J, Heo Y, Jeon BW, Jung M, Kim YH, Lee HH, Roh SH. Structure of recombinant formate dehydrogenase from Methylobacterium extorquens (MeFDH1). Sci Rep 2024; 14:3819. [PMID: 38360844 PMCID: PMC10869683 DOI: 10.1038/s41598-024-54205-7] [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: 07/27/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024] Open
Abstract
Formate dehydrogenase (FDH) is critical for the conversion between formate and carbon dioxide. Despite its importance, the structural complexity of FDH and difficulties in the production of the enzyme have made elucidating its unique physicochemical properties challenging. Here, we purified recombinant Methylobacterium extorquens AM1 FDH (MeFDH1) and used cryo-electron microscopy to determine its structure. We resolved a heterodimeric MeFDH1 structure at a resolution of 2.8 Å, showing a noncanonical active site and a well-embedded Fe-S redox chain relay. In particular, the tungsten bis-molybdopterin guanine dinucleotide active site showed an open configuration with a flexible C-terminal cap domain, suggesting structural and dynamic heterogeneity in the enzyme.
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Affiliation(s)
- Junsun Park
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yoonyoung Heo
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Mingyu Jung
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Soung-Hun Roh
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Leimkühler S. Metal-Containing Formate Dehydrogenases, a Personal View. Molecules 2023; 28:5338. [PMID: 37513211 PMCID: PMC10385643 DOI: 10.3390/molecules28145338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/04/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Mo/W-containing formate dehydrogenases (FDH) catalyzes the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active sites. The metal-containing FDHs are members of the dimethylsulfoxide reductase family of mononuclear molybdenum cofactor (Moco)- or tungsten cofactor (Wco)-containing enzymes. In these enzymes, the active site in the oxidized state comprises a Mo or W atom present in the bis-Moco, which is coordinated by the two dithiolene groups from the two MGD moieties, a protein-derived SeCys or Cys, and a sixth ligand that is now accepted as being a sulfido group. SeCys-containing enzymes have a generally higher turnover number than Cys-containing enzymes. The analogous chemical properties of W and Mo, the similar active sites of W- and Mo-containing enzymes, and the fact that W can replace Mo in some enzymes have led to the conclusion that Mo- and W-containing FDHs have the same reaction mechanism. Details of the catalytic mechanism of metal-containing formate dehydrogenases are still not completely understood and have been discussed here.
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Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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3
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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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4
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Meneghello M, Uzel A, Broc M, Manuel RR, Magalon A, Léger C, Pereira IAC, Walburger A, Fourmond V. Electrochemical Kinetics Support a Second Coordination Sphere Mechanism in Metal-Based Formate Dehydrogenase. Angew Chem Int Ed Engl 2023; 62:e202212224. [PMID: 36465058 PMCID: PMC10107981 DOI: 10.1002/anie.202212224] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/28/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022]
Abstract
Metal-based formate dehydrogenases are molybdenum or tungsten-dependent enzymes that catalyze the interconversion between formate and CO2 . According to the current consensus, the metal ion of the catalytic center in its active form is coordinated by 6 S (or 5 S and 1 Se) atoms, leaving no free coordination sites to which formate could bind to the metal. Some authors have proposed that one of the active site ligands decoordinates during turnover to allow formate binding. Another proposal is that the oxidation of formate takes place in the second coordination sphere of the metal. Here, we have used electrochemical steady-state kinetics to elucidate the order of the steps in the catalytic cycle of two formate dehydrogenases. Our results strongly support the "second coordination sphere" hypothesis.
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Affiliation(s)
- Marta Meneghello
- CNRS, Aix Marseille Université, BIP, IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France
| | - Alexandre Uzel
- CNRS, Aix Marseille Université, BIP, IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France.,Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France
| | - Marianne Broc
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France
| | - Rita R Manuel
- Instituto de Tecnologia Quimica e Biologica Antonio Xavier (ITQB NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France
| | - Christophe Léger
- CNRS, Aix Marseille Université, BIP, IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France
| | - Inês A C Pereira
- Instituto de Tecnologia Quimica e Biologica Antonio Xavier (ITQB NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Anne Walburger
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France
| | - Vincent Fourmond
- CNRS, Aix Marseille Université, BIP, IMM, IM2B, 31 Chemin J. Aiguier, 13009, Marseille, France
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5
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Vilela-Alves G, Manuel RR, Oliveira AR, Pereira IC, Romão MJ, Mota C. Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation. Int J Mol Sci 2022; 24:ijms24010476. [PMID: 36613918 PMCID: PMC9820355 DOI: 10.3390/ijms24010476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO2 to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of DvFdhAB in crystals was confirmed by reduction and reoxidation structural studies.
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Affiliation(s)
- Guilherme Vilela-Alves
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Inês Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria João Romão
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Correspondence:
| | - Cristiano Mota
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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6
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Zhang YQ, Wang ZH, Li M, Liao RZ. Understanding the chemoselectivity switch in CO2 reduction catalyzed by Co and Fe complexes bearing a pentadentate N5 ligand. J Catal 2022. [DOI: 10.1016/j.jcat.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Laun K, Duffus BR, Wahlefeld S, Katz S, Belger D, Hildebrandt P, Mroginski MA, Leimkühler S, Zebger I. Infrared Spectroscopy Elucidates the Inhibitor Binding Sites in a Metal-Dependent Formate Dehydrogenase. Chemistry 2022; 28:e202201091. [PMID: 35662280 PMCID: PMC9804402 DOI: 10.1002/chem.202201091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Indexed: 01/05/2023]
Abstract
Biological carbon dioxide (CO2 ) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.
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Affiliation(s)
- Konstantin Laun
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Benjamin R. Duffus
- Institut für Biochemie und BiologieMolekulare EnzymologieUniversität PotsdamKarl-Liebknecht-Strasse 24–2514476PotsdamGermany
| | - Stefan Wahlefeld
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany,Institut für Technische BiokatalyseTechnische Universität HamburgDenickestr. 1521073HamburgGermany
| | - Sagie Katz
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Dennis Belger
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Peter Hildebrandt
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Maria Andrea Mroginski
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Silke Leimkühler
- Institut für Biochemie und BiologieMolekulare EnzymologieUniversität PotsdamKarl-Liebknecht-Strasse 24–2514476PotsdamGermany
| | - Ingo Zebger
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
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8
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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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9
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Oliveira AR, Mota C, Klymanska K, Biaso F, Romão MJ, Guigliarelli B, Pereira IC. Spectroscopic and Structural Characterization of Reduced Desulfovibrio vulgaris Hildenborough W-FdhAB Reveals Stable Metal Coordination during Catalysis. ACS Chem Biol 2022; 17:1901-1909. [PMID: 35766974 PMCID: PMC9774666 DOI: 10.1021/acschembio.2c00336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO2 reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Desulfovibrio vulgaris Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S]1+ clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S]1+ centers range between -250 and -530 mV. Two distinct WV signals were detected, WDV and WFV, which differ in only the g2-value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of WVI/V was determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate WV state of FdhAB.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cristiano Mota
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Kateryna Klymanska
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Frédéric Biaso
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, Aix Marseille Univ, CNRS, BIP, Marseille 13402, France
| | - Maria João Romão
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,
| | - Bruno Guigliarelli
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, Aix Marseille Univ, CNRS, BIP, Marseille 13402, France,
| | - Inês Cardoso Pereira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal,
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10
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Tran DB, To TH, Tran PD. Mo- and W-molecular catalysts for the H2 evolution, CO2 reduction and N2 fixation. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Abstract
The level of carbon dioxide in the atmosphere has increased in a dangerous way during the past century. Methods to decrease this level are therefore of high interest at present. Inspiration to do so in an efficient way could come from biological systems. Molybdenum-containing formate dehydrogenase (Mo-FDH) is one of the most interesting enzymes in this respect. For example, the reduction potential required is not very low. The normal reaction catalyzed by Mo-FDH is actually the opposite one of oxidizing formate to CO2. However, recent electrochemical studies have shown that the reaction can be reversed by a moderate lowering of the reduction potential. The goal of the present study has been to study the full mechanism of Mo-FDH, particularly in the most interesting direction of reducing CO2, which has not been done before. The methods used are the same as those that have been shown to give excellent results for redox enzymes in all cases they have been tested. The results obtained for Mo-FDH are also in excellent agreement with the experimental results.
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Affiliation(s)
- Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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12
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Liu M, Nazemi A, Taylor MG, Nandy A, Duan C, Steeves AH, Kulik HJ. Large-Scale Screening Reveals That Geometric Structure Matters More Than Electronic Structure in the Bioinspired Catalyst Design of Formate Dehydrogenase Mimics. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Mingjie Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael G. Taylor
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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13
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Meneghello M, Léger C, Fourmond V. Electrochemical Studies of CO 2 -Reducing Metalloenzymes. Chemistry 2021; 27:17542-17553. [PMID: 34506631 DOI: 10.1002/chem.202102702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Indexed: 11/07/2022]
Abstract
Only two enzymes are capable of directly reducing CO2 : CO dehydrogenase, which produces CO at a [NiFe4 S4 ] active site, and formate dehydrogenase, which produces formate at a mononuclear W or Mo active site. Both metalloenzymes are very rapid, energy-efficient and specific in terms of product. They have been connected to electrodes with two different objectives. A series of studies used protein film electrochemistry to learn about different aspects of the mechanism of these enzymes (reactivity with substrates, inhibitors…). Another series focused on taking advantage of the catalytic performance of these enzymes to build biotechnological devices, from CO2 -reducing electrodes to full photochemical devices performing artificial photosynthesis. Here, we review all these works.
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Affiliation(s)
- Marta Meneghello
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, and, Institut Microbiologie, Bioénergies et Biotechnologie, 31 chemin J. Aiguier, 13402, Marseille Cedex 20, France
| | - Christophe Léger
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, and, Institut Microbiologie, Bioénergies et Biotechnologie, 31 chemin J. Aiguier, 13402, Marseille Cedex 20, France
| | - Vincent Fourmond
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, and, Institut Microbiologie, Bioénergies et Biotechnologie, 31 chemin J. Aiguier, 13402, Marseille Cedex 20, France
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14
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Molybdenum-Containing Metalloenzymes and Synthetic Catalysts for Conversion of Small Molecules. Catalysts 2021. [DOI: 10.3390/catal11020217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The energy deficiency and environmental problems have motivated researchers to develop energy conversion systems into a sustainable pathway, and the development of catalysts holds the center of the research endeavors. Natural catalysts such as metalloenzymes have maintained energy cycles on Earth, thus proving themselves the optimal catalysts. In the previous research results, the structural and functional analogs of enzymes and nano-sized electrocatalysts have shown promising activities in energy conversion reactions. Mo ion plays essential roles in natural and artificial catalysts, and the unique electrochemical properties render its versatile utilization as an electrocatalyst. In this review paper, we show the current understandings of the Mo-enzyme active sites and the recent advances in the synthesis of Mo-catalysts aiming for high-performing catalysts.
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15
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Amanullah S, Saha P, Nayek A, Ahmed ME, Dey A. Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis. Chem Soc Rev 2021; 50:3755-3823. [DOI: 10.1039/d0cs01405b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Paramita Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhijit Nayek
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Md Estak Ahmed
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhishek Dey
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
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16
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Yang JY, Kerr TA, Wang XS, Barlow JM. Reducing CO2 to HCO2– at Mild Potentials: Lessons from Formate Dehydrogenase. J Am Chem Soc 2020; 142:19438-19445. [DOI: 10.1021/jacs.0c07965] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jenny Y. Yang
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Tyler A. Kerr
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Xinran S. Wang
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jeffrey M. Barlow
- Department of Chemistry, University of California, Irvine, California 92697, United States
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17
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Oliveira AR, Mota C, Mourato C, Domingos RM, Santos MFA, Gesto D, Guigliarelli B, Santos-Silva T, Romão MJ, Cardoso Pereira IA. Toward the Mechanistic Understanding of Enzymatic CO2 Reduction. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00086] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Cristiano Mota
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cláudia Mourato
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Renato M. Domingos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Marino F. A. Santos
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Diana Gesto
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Bruno Guigliarelli
- Aix Marseille Université, CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Teresa Santos-Silva
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria João Romão
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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18
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Duffus BR, Schrapers P, Schuth N, Mebs S, Dau H, Leimkühler S, Haumann M. Anion Binding and Oxidative Modification at the Molybdenum Cofactor of Formate Dehydrogenase from Rhodobacter capsulatus Studied by X-ray Absorption Spectroscopy. Inorg Chem 2019; 59:214-225. [PMID: 31814403 DOI: 10.1021/acs.inorgchem.9b01613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formate dehydrogenase (FDH) enzymes are versatile catalysts for CO2 conversion. The FDH from Rhodobacter capsulatus contains a molybdenum cofactor with the dithiolene functions of two pyranopterin guanine dinucleotide molecules, a conserved cysteine, and a sulfido group bound at Mo(VI). In this study, we focused on metal oxidation state and coordination changes in response to exposure to O2, inhibitory anions, and redox agents using X-ray absorption spectroscopy (XAS) at the Mo K-edge. Differences in the oxidative modification of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor relative to samples prepared aerobically without inhibitor, such as variations in the relative numbers of sulfido (Mo═S) and oxo (Mo═O) bonds, were observed in the presence of azide (N3-) or cyanate (OCN-). Azide provided best protection against O2, resulting in a quantitatively sulfurated cofactor with a displaced cysteine ligand and optimized formate oxidation activity. Replacement of the cysteine ligand by a formate (HCO2-) ligand at the molybdenum in active enzyme is compatible with our XAS data. Cyanide (CN-) inactivated the enzyme by replacing the sulfido ligand at Mo(VI) with an oxo ligand. Evidence that the sulfido group may become protonated upon molybdenum reduction was obtained. Our results emphasize the role of coordination flexibility at the molybdenum center during inhibitory and catalytic processes of FDH enzymes.
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Affiliation(s)
- Benjamin R Duffus
- Institut für Biochemie und Biologie, Molekulare Enzymologie , Universität Potsdam , Karl-Liebknecht Strasse 24-25 , 14476 Potsdam , Germany
| | - Peer Schrapers
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Nils Schuth
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Stefan Mebs
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Holger Dau
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | - Silke Leimkühler
- Institut für Biochemie und Biologie, Molekulare Enzymologie , Universität Potsdam , Karl-Liebknecht Strasse 24-25 , 14476 Potsdam , Germany
| | - Michael Haumann
- Institut für Experimentalphysik , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
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19
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Schneider CR, Lewis LC, Shafaat HS. The good, the neutral, and the positive: buffer identity impacts CO 2 reduction activity by nickel(ii) cyclam. Dalton Trans 2019; 48:15810-15821. [PMID: 31560360 PMCID: PMC6843992 DOI: 10.1039/c9dt03114f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Development of new synthetic catalysts for CO2 reduction has been a central focus of chemical research efforts towards mitigating rising global carbon dioxide levels. In parallel with generating new molecular systems, characterization and benchmarking of these compounds across well-defined catalytic conditions are essential. Nickel(ii) cyclam is known to be an active catalyst for CO2 reduction to CO. The degree of selectivity and activity has been found to differ widely across electrodes used and upon modification of the ligand environment, though without a molecular-level understanding of this variation. Moreover, while proton transfer is key for catalytic activity, the effects of varying the nature of the proton donor remain unclear. In this work, a systematic investigation of the electrochemical and light-driven catalytic behaviour of nickel(ii) cyclam under different aqueous reaction conditions has been performed. The activity and selectivity are seen to vary widely depending on the nature of the buffering agent, even at a constant pH, highlighting the importance of proton transfer for catalysis. Buffer binding to the nickel center is negatively correlated with selectivity, and cationic buffers show high levels of selectivity and activity. These results are discussed in the context of molecular design principles for developing increasingly efficient and selective catalysts. Moreover, identifying these key contributors towards activity has implications for understanding the role of the conserved secondary coordination environments in naturally occurring CO2-reducing enzymes, including carbon monoxide dehydrogenase and formate dehydrogenase.
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Affiliation(s)
- Camille R Schneider
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Luke C Lewis
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
| | - Hannah S Shafaat
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA and Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
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20
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Sümbelli Y, Biçen Ünlüer Ö, Ersöz A, Say R. Synergistic effect of binanoenzyme and cryogel column on the production of formic acid from carbondioxide. J IND ENG CHEM 2019. [DOI: 10.1016/j.jiec.2019.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:molecules24132462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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22
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Seo J, Shearer J, Williard PG, Kim E. Reactivity of a biomimetic W(iv) bis-dithiolene complex with CO2 leading to formate production and structural rearrangement. Dalton Trans 2019; 48:17441-17444. [DOI: 10.1039/c9dt03906f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mononuclear W(iv) bis-dithiolene complex reduces CO2 to formate while generating a dinuclear W(v) complex.
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Affiliation(s)
- Junhyeok Seo
- Department of Chemistry
- Gwangju Institute of Science and Technology
- Gwangju 61005
- Republic of Korea
| | - Jason Shearer
- Department of Chemistry
- Trinity University
- San Antonio
- USA
| | | | - Eunsuk Kim
- Department of Chemistry
- Brown University
- Providence
- USA
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23
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Dong G, Ryde U. Reaction mechanism of formate dehydrogenase studied by computational methods. J Biol Inorg Chem 2018; 23:1243-1254. [PMID: 30173398 DOI: 10.1007/s00775-018-1608-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/22/2018] [Indexed: 02/05/2023]
Abstract
Formate dehydrogenases (FDHs) are metalloenzymes that catalyse the reversible conversion of formate to carbon dioxide. Since such a process may be used to combat the greenhouse effect, FDHs have been extensively studied by experimental and theoretical methods. However, the reaction mechanism is still not clear; instead five putative mechanisms have been suggested. In this work, the reaction mechanism of FDH was studied by computational methods. Combined quantum mechanical and molecular mechanic (QM/MM) optimisations were performed to obtain the geometries. To get more accurate energies and obtain a detailed account of the surroundings, big-QM calculations with a very large (1121 atoms) QM region were performed. Our results indicate that the formate substrate does not coordinate directly to Mo when it enters the oxidised active site of the FDH, but instead resides in the second coordination sphere. The sulfido ligand abstracts a hydride ion from the substrate, giving a Mo(IV)-SH state and a thiocarbonate ion attached to Cys196. The latter releases CO2 when the active site is oxidised back to the resting (MoVI) state. This mechanism is supported by recent experimental studies.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00, Lund, Sweden
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 514041, Guangdong, People's Republic of China
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00, Lund, Sweden.
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24
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Ferreira P, Cerqueira NM, Brás NF, Fernandes PA, Ramos MJ. Parametrization of Molybdenum Cofactors for the AMBER Force Field. J Chem Theory Comput 2018; 14:2538-2548. [DOI: 10.1021/acs.jctc.8b00137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pedro Ferreira
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, s/n, 4169-007 Porto, Portugal
| | - Nuno M.F.S.A. Cerqueira
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, s/n, 4169-007 Porto, Portugal
| | - Natércia F. Brás
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, s/n, 4169-007 Porto, Portugal
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25
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Elrod LT, Kim E. Lewis Acid Assisted Nitrate Reduction with Biomimetic Molybdenum Oxotransferase Complex. Inorg Chem 2018; 57:2594-2602. [PMID: 29443517 DOI: 10.1021/acs.inorgchem.7b02956] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reduction of nitrate (NO3-) to nitrite (NO2-) is of significant biological and environmental importance. While MoIV(O) and MoVI(O)2 complexes that mimic the active site structure of nitrate reducing enzymes are prevalent, few of these model complexes can reduce nitrate to nitrite through oxygen atom transfer (OAT) chemistry. We present a novel strategy to induce nitrate reduction chemistry of a previously known catalyst MoIV(O)(SN)2 (2), where SN = bis(4- tert-butylphenyl)-2-pyridylmethanethiolate, that is otherwise incapable of achieving OAT with nitrate. Addition of nitrate with the Lewis acid Sc(OTf)3 (OTf = trifluoromethanesulfonate) to 2 results in an immediate and clean conversion of 2 to MoVI(O)2(SN)2 (1). The Lewis acid additive further reacts with the OAT product, nitrite, to form N2O and O2. This work highlights the ability of Sc3+ additives to expand the reactivity scope of an existing MoIV(O) complex together with which Sc3+ can convert nitrate to stable gaseous molecules.
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Affiliation(s)
- Lee Taylor Elrod
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Eunsuk Kim
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
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26
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Cerqueira NMFSA, Fernandes PA, Ramos MJ. Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation. Chemphyschem 2018; 19:669-689. [DOI: 10.1002/cphc.201700339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/22/2017] [Indexed: 01/12/2023]
Affiliation(s)
- N. M. F. S. A. Cerqueira
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - P. A. Fernandes
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - M. J. Ramos
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
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27
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Lalinde E, Lara R, López IP, Moreno MT, Alfaro-Arnedo E, Pichel JG, Piñeiro-Hermida S. Benzothiazole-Based Cycloplatinated Chromophores: Synthetic, Optical, and Biological Studies. Chemistry 2018; 24:2440-2456. [PMID: 29219223 DOI: 10.1002/chem.201705267] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Indexed: 02/05/2023]
Abstract
Cycloplatinated complexes based on 2-(4-substituted)benzothiazole ligands of type [Pt(R-PBT-κC,N)Cl(L)] (PBT=2-phenylbenzothiazole; R=Br (1), Me2 N (2); L=dimethyl sulfoxide (DMSO; a), 1,3,5- triaza-7-phosphaadamantane (PTA; b), triphenylphosphine 3,3',3''-trisulfonate (TPPTS; c)) and [Pt(Br-PBT-κC)Cl(PTA)2 ] (3) are presented. On the basis of the photophysical data and time-dependent (TD)-DFT calculations (1 a and 2 a), the low-lying transitions (absorption and emission) were associated with ligand-center (LC) charge transfer, with minor metal-to-ligand charge transfer (MLCT), and intraligand charge transfer (ILCT) [Me2 N-PBT→PBT] excited states, respectively. Simultaneous fluorescence/phosphorescence bands were found in fluid solutions (and also in the solid state for 2 a), which become dominated by triplet emission bands in rigid media at 77 K. The effect of the concentration on emissive behavior of 2 a, b indicated the occurrence of aggregation-induced luminescence properties related to the occurrence of metal-metal and π⋅⋅⋅π interactions, which are more enhanced in 2 a because of the less bulky DMSO ligand. The behavior of 2 a toward para-toluenesulfonic acid (PTSA) in aerated acetonitrile and to hydrogen chloride gas in the solid state has been evaluated, thus showing a clear reversible change between the 1 ILCT and 3 LC/3 MLCT states due to protonation of the NMe2 group (theoretical calculations on 2 a-H+ ). Solid 2 a undergoes a surprising oxidation of the PtII center to PtIV with concomitant deoxygenation of DMSO, under prolonged reaction with hydrogen chloride gas to afford the PtIV /dimethyl sulfide complex (mer-[Pt(Me2 N-PBT-κC,N)Cl3 (SMe2 )]; mer-4), which evolves in solution to fac-4, as confirmed by X-ray studies. Cytotoxic activity studies on A549 and HeLa cell lines indicated cytotoxic activity of 1 b and 2 a, b. In addition, fluorescent cell microscopy revealed cytoplasmic staining, more visible in perinuclear areas. Inhibition of tubulin polymerization by 1 b in both cells is presented as a preliminary mechanism of its cytotoxic action.
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Affiliation(s)
- Elena Lalinde
- Departamento de Química-Centro de Síntesis Química de La Rioja (CISQ), Universidad de La Rioja, 26006, Logroño, Spain
| | - Rebeca Lara
- Departamento de Química-Centro de Síntesis Química de La Rioja (CISQ), Universidad de La Rioja, 26006, Logroño, Spain
| | - Icíar P López
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, 26006, Logroño, Spain
| | - M Teresa Moreno
- Departamento de Química-Centro de Síntesis Química de La Rioja (CISQ), Universidad de La Rioja, 26006, Logroño, Spain
| | - Elvira Alfaro-Arnedo
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, 26006, Logroño, Spain
| | - José G Pichel
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, 26006, Logroño, Spain
| | - Sergio Piñeiro-Hermida
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, 26006, Logroño, Spain
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28
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Cerqueira NMFSA, Fernandes PA, Ramos MJ. Visualizing the Microscopic World. Interdiscip Sci 2017; 10:105-110. [PMID: 28791579 DOI: 10.1007/s12539-017-0255-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 06/30/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
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29
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Robinson WE, Bassegoda A, Reisner E, Hirst J. Oxidation-State-Dependent Binding Properties of the Active Site in a Mo-Containing Formate Dehydrogenase. J Am Chem Soc 2017; 139:9927-9936. [PMID: 28635274 PMCID: PMC5532686 DOI: 10.1021/jacs.7b03958] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molybdenum-containing formate dehydrogenase H from Escherichia coli (EcFDH-H) is a powerful model system for studies of the reversible reduction of CO2 to formate. However, the mechanism of FDH catalysis is currently under debate, and whether the primary Mo coordination sphere remains saturated or one of the ligands dissociates to allow direct substrate binding during turnover is disputed. Herein, we describe how oxidation-state-dependent changes at the active site alter its inhibitor binding properties. Using protein film electrochemistry, we show that formate oxidation by EcFDH-H is inhibited strongly and competitively by N3-, OCN-, SCN-, NO2-, and NO3-, whereas CO2 reduction is inhibited only weakly and not competitively. During catalysis, the Mo center cycles between the formal Mo(VI)═S and Mo(IV)-SH states, and by modeling chronoamperometry data recorded at different potentials and substrate and inhibitor concentrations, we demonstrate that both formate oxidation and CO2 reduction are inhibited by selective inhibitor binding to the Mo(VI)═S state. The strong dependence of inhibitor-binding affinity on both Mo oxidation state and inhibitor electron-donor strength indicates that inhibitors (and substrates) bind directly to the Mo center. We propose that inhibitors bind to the Mo following dissociation of a selenocysteine ligand to create a vacant coordination site for catalysis and close by considering the implications of our data for the mechanisms of formate oxidation and CO2 reduction.
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Affiliation(s)
- William E Robinson
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Arnau Bassegoda
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
| | - Erwin Reisner
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
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Roy S, Sharma B, Pécaut J, Simon P, Fontecave M, Tran PD, Derat E, Artero V. Molecular Cobalt Complexes with Pendant Amines for Selective Electrocatalytic Reduction of Carbon Dioxide to Formic Acid. J Am Chem Soc 2017; 139:3685-3696. [PMID: 28206761 DOI: 10.1021/jacs.6b11474] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report here on a new series of CO2-reducing molecular catalysts based on Earth-abundant elements that are very selective for the production of formic acid in dimethylformamide (DMF)/water mixtures (Faradaic efficiency of 90 ± 10%) at moderate overpotentials (500-700 mV in DMF measured at the middle of the catalytic wave). The [CpCo(PR2NR'2)I]+ compounds contain diphosphine ligands, PR2NR'2, with two pendant amine residues that act as proton relays during CO2-reduction catalysis and tune their activity. Four different PR2NR'2 ligands with cyclohexyl or phenyl substituents on phosphorus and benzyl or phenyl substituents on nitrogen were employed, and the compound with the most electron-donating phosphine ligand and the most basic amine functions performs best among the series, with turnover frequency >1000 s-1. State-of-the-art benchmarking of catalytic performances ranks this new class of cobalt-based complexes among the most promising CO2-to-formic acid reducing catalysts developed to date; addressing the stability issues would allow further improvement. Mechanistic studies and density functional theory simulations confirmed the role of amine groups for stabilizing key intermediates through hydrogen bonding with water molecules during hydride transfer from the Co center to the CO2 molecule.
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Affiliation(s)
- Souvik Roy
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes , CEA, CNRS, 17 rue des Martyrs, 38000 Grenoble, France
| | - Bhaskar Sharma
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Universités , UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Jacques Pécaut
- Reconnaissance Ionique et Chimie de Coordination, DRF-INAC-SyMMES, Université Grenoble Alpes , CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
| | - Philippe Simon
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie , CNRS UMR 8229, 11 place Marcelin Berthelot, 75005 Paris, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie , CNRS UMR 8229, 11 place Marcelin Berthelot, 75005 Paris, France
| | - Phong D Tran
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes , CEA, CNRS, 17 rue des Martyrs, 38000 Grenoble, France.,Department of Advanced Materials Science and Nanotechnology, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay, 122102 Hanoi, Vietnam
| | - Etienne Derat
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Universités , UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes , CEA, CNRS, 17 rue des Martyrs, 38000 Grenoble, France
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31
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Maia LB, Moura I, Moura JJ. Molybdenum and tungsten-containing formate dehydrogenases: Aiming to inspire a catalyst for carbon dioxide utilization. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.07.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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32
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Bastola KP, Guragain YN, Bhadriraju V, Vadlani PV. Evaluation of Standards and Interfering Compounds in the Determination of Phenolics by Folin-Ciocalteu Assay Method for Effective Bioprocessing of Biomass. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ajac.2017.86032] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Maia LB, Fonseca L, Moura I, Moura JJG. Reduction of Carbon Dioxide by a Molybdenum-Containing Formate Dehydrogenase: A Kinetic and Mechanistic Study. J Am Chem Soc 2016; 138:8834-46. [PMID: 27348246 DOI: 10.1021/jacs.6b03941] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbon dioxide accumulation is a major concern for the ecosystems, but its abundance and low cost make it an interesting source for the production of chemical feedstocks and fuels. However, the thermodynamic and kinetic stability of the carbon dioxide molecule makes its activation a challenging task. Studying the chemistry used by nature to functionalize carbon dioxide should be helpful for the development of new efficient (bio)catalysts for atmospheric carbon dioxide utilization. In this work, the ability of Desulfovibrio desulfuricans formate dehydrogenase (Dd FDH) to reduce carbon dioxide was kinetically and mechanistically characterized. The Dd FDH is suggested to be purified in an inactive form that has to be activated through a reduction-dependent mechanism. A kinetic model of a hysteretic enzyme is proposed to interpret and predict the progress curves of the Dd FDH-catalyzed reactions (initial lag phase and subsequent faster phase). Once activated, Dd FDH is able to efficiently catalyze, not only the formate oxidation (kcat of 543 s(-1), Km of 57.1 μM), but also the carbon dioxide reduction (kcat of 46.6 s(-1), Km of 15.7 μM), in an overall reaction that is thermodynamically and kinetically reversible. Noteworthy, both Dd FDH-catalyzed formate oxidation and carbon dioxide reduction are completely inactivated by cyanide. Current FDH reaction mechanistic proposals are discussed and a different mechanism is here suggested: formate oxidation and carbon dioxide reduction are proposed to proceed through hydride transfer and the sulfo group of the oxidized and reduced molybdenum center, Mo(6+)═S and Mo(4+)-SH, are suggested to be the direct hydride acceptor and donor, respectively.
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Affiliation(s)
- Luisa B Maia
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Luis Fonseca
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Isabel Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - José J G Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
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34
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Hartmann T, Schrapers P, Utesch T, Nimtz M, Rippers Y, Dau H, Mroginski MA, Haumann M, Leimkühler S. The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C–H Bond Cleavage and Oxygen Atom Transfer Reactions. Biochemistry 2016; 55:2381-9. [DOI: 10.1021/acs.biochem.6b00002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tobias Hartmann
- Department
of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam, Germany
| | - Peer Schrapers
- Institute
of Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Tillmann Utesch
- Institute
of Chemistry, Technical University of Berlin, Straße des 17. Juni135, 10623 Berlin, Germany
| | - Manfred Nimtz
- Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Yvonne Rippers
- Institute
of Chemistry, Technical University of Berlin, Straße des 17. Juni135, 10623 Berlin, Germany
| | - Holger Dau
- Institute
of Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Maria Andrea Mroginski
- Institute
of Chemistry, Technical University of Berlin, Straße des 17. Juni135, 10623 Berlin, Germany
| | - Michael Haumann
- Institute
of Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Silke Leimkühler
- Department
of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam, Germany
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35
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Sultana S, Chandra Sahoo P, Martha S, Parida K. A review of harvesting clean fuels from enzymatic CO2 reduction. RSC Adv 2016. [DOI: 10.1039/c6ra05472b] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This review has summarised single enzyme, multi enzymatic and semiconducting nanomaterial integrated enzymatic systems for CO2 conversion to clean fuels.
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Affiliation(s)
- Sabiha Sultana
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Prakash Chandra Sahoo
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Satyabadi Martha
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Kulamani Parida
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
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36
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Cerqueira NMFSA, Gonzalez PJ, Fernandes PA, Moura JJG, Ramos MJ. Periplasmic nitrate reductase and formate dehydrogenase: similar molecular architectures with very different enzymatic activities. Acc Chem Res 2015; 48:2875-84. [PMID: 26509703 DOI: 10.1021/acs.accounts.5b00333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It is remarkable how nature has been able to construct enzymes that, despite sharing many similarities, have simple but key differences that tune them for completely different functions in living cells. Periplasmic nitrate reductase (Nap) and formate dehydrogenase (Fdh) from the DMSOr family are representative examples of this. Both enzymes share almost identical three-dimensional protein foldings and active sites, in terms of coordination number, geometry and nature of the ligands. The substrates of both enzymes (nitrate and formate) are polyatomic anions that also share similar charge and stereochemistry. In terms of the catalytic mechanism, both enzymes have a common activation mechanism (the sulfur-shift mechanism) that ensures a constant coordination number around the metal ion during the catalytic cycle. In spite of these similarities, they catalyze very different reactions: Nap abstracts an oxygen atom from nitrate releasing nitrite, whereas FdH catalyzes a hydrogen atom transfer from formate and releases carbon dioxide. In this Account, a critical analysis of structure, function, and catalytic mechanism of the molybdenum enzymes periplasmic nitrate reductase (Nap) and formate dehydrogenase (Fdh) is presented. We conclude that the main structural driving force that dictates the type of reaction, catalyzed by each enzyme, is a key difference on one active site residue that is located in the top region of the active sites of both enzymes. In both enzymes, the active site is centered on the metal ion of the cofactor (Mo in Nap and Mo or W in Fdh) that is coordinated by four sulfur atoms from two pyranopterin guanosine dinucleotide (PGD) molecules and by a sulfido. However, while in Nap there is a Cys directly coordinated to the Mo ion, in FdH there is a SeCys instead. In Fdh there is also an important His that interacts very closely with the SeCys, whereas in Nap the same position is occupied by a Met. The role of Cys in Nap and SeCys in FdH is similar in both enzymes; however, Met and His have different roles. His participates directly on catalysis, and it is therefore detrimental for the catalytic cycle of FdH. Met only participates in substrate binding. We concluded that this small but key difference dictates the type of reaction that is catalyzed by each enzyme. In addition, it allows explaining why formate can bind in the Nap active site in the same way as the natural substrate (nitrate), but the reaction becomes stalled afterward.
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Affiliation(s)
- Nuno M. F. S. A. Cerqueira
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pablo J. Gonzalez
- REQUIMTE/UCIBIO,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Pedro A. Fernandes
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - José J. G. Moura
- REQUIMTE/UCIBIO,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Maria João Ramos
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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37
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Leimkühler S, Iobbi-Nivol C. Bacterial molybdoenzymes: old enzymes for new purposes. FEMS Microbiol Rev 2015; 40:1-18. [PMID: 26468212 DOI: 10.1093/femsre/fuv043] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2015] [Indexed: 02/06/2023] Open
Abstract
Molybdoenzymes are widespread in eukaryotic and prokaryotic organisms where they play crucial functions in detoxification reactions in the metabolism of humans and bacteria, in nitrate assimilation in plants and in anaerobic respiration in bacteria. To be fully active, these enzymes require complex molybdenum-containing cofactors, which are inserted into the apoenzymes after folding. For almost all the bacterial molybdoenzymes, molybdenum cofactor insertion requires the involvement of specific chaperones. In this review, an overview on the molybdenum cofactor biosynthetic pathway is given together with the role of specific chaperones dedicated for molybdenum cofactor insertion and maturation. Many bacteria are involved in geochemical cycles on earth and therefore have an environmental impact. The roles of molybdoenzymes in bioremediation and for environmental applications are presented.
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Affiliation(s)
- Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476 Potsdam, Germany
| | - Chantal Iobbi-Nivol
- The Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS, Aix Marseille Université, 13402 Marseille cedex 20, France
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38
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Omajali JB, Mikheenko IP, Merroun ML, Wood J, Macaskie LE. Characterization of intracellular palladium nanoparticles synthesized by Desulfovibrio desulfuricans and Bacillus benzeovorans. JOURNAL OF NANOPARTICLE RESEARCH : AN INTERDISCIPLINARY FORUM FOR NANOSCALE SCIENCE AND TECHNOLOGY 2015; 17:264. [PMID: 27004043 PMCID: PMC4779138 DOI: 10.1007/s11051-015-3067-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/03/2015] [Indexed: 05/24/2023]
Abstract
Early studies have focused on the synthesis of palladium nanoparticles within the periplasmic layer or on the outer membrane of Desulfovibrio desulfuricans and on the S-layer protein of Bacillus sphaericus. However, it has remained unclear whether the synthesis of palladium nanoparticles also takes place in the bacterial cell cytoplasm. This study reports the use of high-resolution scanning transmission electron microscopy with a high-angle annular dark field detector and energy dispersive X-ray spectrometry attachment to investigate the intracellular synthesis of palladium nanoparticles (Pd NPs). We show the intracellular synthesis of Pd NPs within cells of two anaerobic strains of D. desulfuricans and an aerobic strain of B. benzeovorans using hydrogen and formate as electron donors. The Pd nanoparticles were small and largely monodispersed, between 0.2 and 8 nm, occasionally from 9 to 12 nm with occasional larger nanoparticles. With D. desulfuricans NCIMB 8307 (but not D. desulfuricans NCIMB 8326) and with B. benzeovorans NCIMB 12555, the NPs were larger when made at the expense of formate, co-localizing with phosphate in the latter, and were crystalline, but were amorphous when made with H2, with no phosphorus association. The intracellular Pd nanoparticles were mainly icosahedrons with surfaces comprising {111} facets and about 5 % distortion when compared with that of bulk palladium. The particles were more concentrated in the cell cytoplasm than the cell wall, outer membrane, or periplasm. We provide new evidence for synthesis of palladium nanoparticles within the cytoplasm of bacteria, which were confirmed to maintain cellular integrity during this synthesis.
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Affiliation(s)
- Jacob B. Omajali
- />Unit of Functional Bionanomaterials, School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Iryna P. Mikheenko
- />Unit of Functional Bionanomaterials, School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Mohamed L. Merroun
- />Department of Microbiology, Faculty of Sciences, University of Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Joseph Wood
- />School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Lynne E. Macaskie
- />Unit of Functional Bionanomaterials, School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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39
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Bio-inspired mechanistic insights into CO2 reduction. Curr Opin Chem Biol 2015; 25:103-9. [DOI: 10.1016/j.cbpa.2014.12.022] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 11/17/2022]
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40
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Schrapers P, Hartmann T, Kositzki R, Dau H, Reschke S, Schulzke C, Leimkühler S, Haumann M. Sulfido and cysteine ligation changes at the molybdenum cofactor during substrate conversion by formate dehydrogenase (FDH) from Rhodobacter capsulatus. Inorg Chem 2015; 54:3260-71. [PMID: 25803130 DOI: 10.1021/ic502880y] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Formate dehydrogenase (FDH) enzymes are attractive catalysts for potential carbon dioxide conversion applications. The FDH from Rhodobacter capsulatus (RcFDH) binds a bis-molybdopterin-guanine-dinucleotide (bis-MGD) cofactor, facilitating reversible formate (HCOO(-)) to CO2 oxidation. We characterized the molecular structure of the active site of wildtype RcFDH and protein variants using X-ray absorption spectroscopy (XAS) at the Mo K-edge. This approach has revealed concomitant binding of a sulfido ligand (Mo=S) and a conserved cysteine residue (S(Cys386)) to Mo(VI) in the active oxidized molybdenum cofactor (Moco), retention of such a coordination motif at Mo(V) in a chemically reduced enzyme, and replacement of only the S(Cys386) ligand by an oxygen of formate upon Mo(IV) formation. The lack of a Mo=S bond in RcFDH expressed in the absence of FdsC implies specific metal sulfuration by this bis-MGD binding chaperone. This process still functioned in the Cys386Ser variant, showing no Mo-S(Cys386) ligand, but retaining a Mo=S bond. The C386S variant and the protein expressed without FdsC were inactive in formate oxidation, supporting that both Mo-ligands are essential for catalysis. Low-pH inhibition of RcFDH was attributed to protonation at the conserved His387, supported by the enhanced activity of the His387Met variant at low pH, whereas inactive cofactor species showed sulfido-to-oxo group exchange at the Mo ion. Our results support that the sulfido and S(Cys386) ligands at Mo and a hydrogen-bonded network including His387 are crucial for positioning, deprotonation, and oxidation of formate during the reaction cycle of RcFDH.
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Affiliation(s)
- Peer Schrapers
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Tobias Hartmann
- ‡Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Ramona Kositzki
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Holger Dau
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Stefan Reschke
- ‡Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Carola Schulzke
- §Institut für Biochemie, Bioanorganische Chemie, Ernst-Moritz-Arndt-Universität Greifswald, 17487 Greifswald, Germany
| | - Silke Leimkühler
- ‡Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Michael Haumann
- †Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
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41
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Cerqueira NMFSA, Pakhira B, Sarkar S. Theoretical studies on mechanisms of some Mo enzymes. J Biol Inorg Chem 2015; 20:323-35. [DOI: 10.1007/s00775-015-1237-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/05/2015] [Indexed: 11/30/2022]
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42
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Gan L, Jennings D, Laureanti J, Jones AK. Biomimetic Complexes for Production of Dihydrogen and Reduction of CO2. TOP ORGANOMETAL CHEM 2015. [DOI: 10.1007/3418_2015_146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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43
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Reimann J, Jetten MSM, Keltjens JT. Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane. Met Ions Life Sci 2015; 15:257-313. [PMID: 25707470 DOI: 10.1007/978-3-319-12415-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.
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Affiliation(s)
- Joachim Reimann
- Department of Microbiology, Institute of Wetland and Water Research (IWWR), Radboud University of Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands,
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44
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Hartmann T, Schwanhold N, Leimkühler S. Assembly and catalysis of molybdenum or tungsten-containing formate dehydrogenases from bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1090-100. [PMID: 25514355 DOI: 10.1016/j.bbapap.2014.12.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/04/2014] [Accepted: 12/06/2014] [Indexed: 11/28/2022]
Abstract
The global carbon cycle depends on the biological transformations of C1 compounds, which include the reductive incorporation of CO₂into organic molecules (e.g. in photosynthesis and other autotrophic pathways), in addition to the production of CO₂from formate, a reaction that is catalyzed by formate dehydrogenases (FDHs). FDHs catalyze, in general, the oxidation of formate to CO₂and H⁺. However, selected enzymes were identified to act as CO₂reductases, which are able to reduce CO₂to formate under physiological conditions. This reaction is of interest for the generation of formate as a convenient storage form of H₂for future applications. Cofactor-containing FDHs are found in anaerobic bacteria and archaea, in addition to facultative anaerobic or aerobic bacteria. These enzymes are highly diverse and employ different cofactors such as the molybdenum cofactor (Moco), FeS clusters and flavins, or cytochromes. Some enzymes include tungsten (W) in place of molybdenum (Mo) at the active site. For catalytic activity, a selenocysteine (SeCys) or cysteine (Cys) ligand at the Mo atom in the active site is essential for the reaction. This review will focus on the characterization of Mo- and W-containing FDHs from bacteria, their active site structure, subunit compositions and its proposed catalytic mechanism. We will give an overview on the different mechanisms of substrate conversion available so far, in addition to providing an outlook on bio-applications of FDHs. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Tobias Hartmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany
| | - Nadine Schwanhold
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany.
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Molybdenum and tungsten-dependent formate dehydrogenases. J Biol Inorg Chem 2014; 20:287-309. [DOI: 10.1007/s00775-014-1218-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/09/2014] [Indexed: 11/25/2022]
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Oldenhof S, Lutz M, de Bruin B, Ivar van der Vlugt J, Reek JNH. Dehydrogenation of formic acid by Ir-bisMETAMORPhos complexes: experimental and computational insight into the role of a cooperative ligand. Chem Sci 2014; 6:1027-1034. [PMID: 29560190 PMCID: PMC5811074 DOI: 10.1039/c4sc02555e] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/21/2014] [Indexed: 01/15/2023] Open
Abstract
The synthesis of Ir-complexes with three bisMETAMORPhos ligands is reported. The activity of these systems towards HCOOH dehydrogenation and the dual role of the ligand during catalysis is discussed, using spectroscopic and computational methods.
The synthesis and tautomeric nature of three xanthene-based bisMETAMORPhos ligands (La–Lc) is reported. Coordination of these bis(sulfonamidophosphines) to Ir(acac)(cod) initially leads to the formation of IrI(LH) species (1a), which convert via formal oxidative addition of the ligand to IrIII(L) monohydride complexes 2a–c. The rate for this step strongly depends on the ligand employed. IrIII complexes 2a–c were applied in the base-free dehydrogenation of formic acid, reaching turnover frequencies of 3090, 877 and 1791 h–1, respectively. The dual role of the ligand in the mechanism of the dehydrogenation reaction was studied by 1H and 31P NMR spectroscopy and DFT calculations. Besides functioning as an internal base, bisMETAMORPhos also assists in the pre-assembly of formic acid within the Ir-coordination sphere and aids in stabilizing the rate-determining transition state through hydrogen-bonding.
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Affiliation(s)
- Sander Oldenhof
- van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH , Amsterdam , The Netherlands .
| | - Martin Lutz
- Bijvoet Center for Biomolecular Research , Utrecht University , Padualaan 8 , 3584 CH , Utrecht , The Netherlands
| | - Bas de Bruin
- van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH , Amsterdam , The Netherlands .
| | - Jarl Ivar van der Vlugt
- van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH , Amsterdam , The Netherlands .
| | - Joost N H Reek
- van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH , Amsterdam , The Netherlands .
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Aranda J, Cerqueira NMFSA, Fernandes PA, Roca M, Tuñon I, Ramos MJ. The catalytic mechanism of carboxylesterases: a computational study. Biochemistry 2014; 53:5820-9. [PMID: 25101647 DOI: 10.1021/bi500934j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic mechanism of carboxylesterases (CEs, EC 3.1.1.1) is explored by computational means. CEs hydrolyze ester, amide, and carbamate bonds found in xenobiotics and endobiotics. They can also perform transesterification, a reaction important, for instance, in cholesterol homeostasis. The catalytic mechanisms with three different substrates (ester, thioester, and amide) have been established at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory. It was found that the reactions proceed through a mechanism involving four steps instead of two as is generally proposed: (i) nucleophilic attack of serine to the substrate, forming the first tetrahedral intermediate, (ii) formation of the acyl-enzyme complex concomitant with the release of the alcohol product, (iii) nucleophilic attack of a water or alcohol molecule forming the second tetrahedral intermediate, and (iv) the release of the second product of the reaction. The results agree very well with the available experimental data and show that the hydrolytic and the transesterification reactions are competitive processes when the substrate is an ester. In all the other studied substrates (thioester or amide), the hydrolytic and transesterification process are less favorable and some of them might not even take place under in vivo conditions.
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Affiliation(s)
- J Aranda
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Ribeiro JV, Cerqueira NMFSA, Fernandes PA, Ramos MJ. chem-path-tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures. Chem Biol Drug Des 2014; 84:44-53. [DOI: 10.1111/cbdd.12349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/16/2014] [Accepted: 04/20/2014] [Indexed: 01/25/2023]
Affiliation(s)
- João V. Ribeiro
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
| | - N. M. F. S. A. Cerqueira
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
| | - Pedro A. Fernandes
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
| | - Maria J. Ramos
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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Böhmer N, Hartmann T, Leimkühler S. The chaperone FdsC for Rhodobacter capsulatus formate dehydrogenase binds the bis-molybdopterin guanine dinucleotide cofactor. FEBS Lett 2014; 588:531-7. [PMID: 24444607 DOI: 10.1016/j.febslet.2013.12.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 11/25/2022]
Abstract
Molybdoenzymes are complex enzymes in which the molybdenum cofactor (Moco) is deeply buried in the enzyme. Most molybdoenzymes contain a specific chaperone for the insertion of Moco. For the formate dehydrogenase FdsGBA from Rhodobacter capsulatus the two chaperones FdsC and FdsD were identified to be essential for enzyme activity, but are not a subunit of the mature enzyme. Here, we purified and characterized the FdsC protein after heterologous expression in Escherichia coli. We were able to copurify FdsC with the bound Moco derivate bis-molybdopterin guanine dinucleotide. This cofactor successfully was used as a source to reconstitute the activity of molybdoenzymes.
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Affiliation(s)
- Nadine Böhmer
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany
| | - Tobias Hartmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, D-14476 Potsdam, Germany.
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