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Vilela-Alves G, Rebelo Manuel R, Pedrosa N, Cardoso Pereira IA, Romão MJ, Mota C. Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2024; 80:98-106. [PMID: 38699971 PMCID: PMC11134731 DOI: 10.1107/s2053230x24003911] [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: 02/26/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO2 to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine Sδ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO2 reduction, together with an increased sensitivity to oxygen inactivation.
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Affiliation(s)
- Guilherme Vilela-Alves
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Maria João Romão
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cristiano Mota
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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2
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Duffus BR, Gauglitz M, Teutloff C, Leimkühler S. Redox potentials elucidate the electron transfer pathway of NAD +-dependent formate dehydrogenases. J Inorg Biochem 2024; 253:112487. [PMID: 38306887 DOI: 10.1016/j.jinorgbio.2024.112487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024]
Abstract
Metal-dependent, nicotine adenine dinucleotide (NAD+)-dependent formate dehydrogenases (FDHs) are complex metalloenzymes coupling biochemical transformations through intricate electron transfer pathways. Rhodobacter capsulatus FDH is a model enzyme for understanding coupled catalysis, in that reversible CO2 reduction and formate oxidation are linked to a flavin mononuclotide (FMN)-bound diaphorase module via seven iron-sulfur (FeS) clusters as a dimer of heterotetramers. Catalysis occurs at a bis-metal-binding pterin (Mo) binding two molybdopterin guanine dinucleotides (bis-MGD), a protein-based Cys residue and a participatory sulfido ligand. Insights regarding the proposed electron transfer mechanism between the bis-MGD and the FMN have been complicated by the discovery that an alternative pathway might occur via intersubunit electron transfer between two [4Fe4S] clusters within electron transfer distance. To clarify this difference, the redox potentials of the bis-MGD and the FeS clusters were determined via redox titration by EPR spectroscopy. Redox potentials for the bis-MGD cofactor and five of the seven FeS clusters could be assigned. Furthermore, substitution of the active site residue Lys295 with Ala resulted in altered enzyme kinetics, primarily due to a more negative redox potential of the A1 [4Fe4S] cluster. Finally, characterization of the monomeric FdsGBAD heterotetramer exhibited slightly decreased formate oxidation activity and similar iron-sulfur clusters reduced relative to the dimeric heterotetramer. Comparison of the measured redox potentials relative to structurally defined FeS clusters support a mechanism by which electron transfer occurs within a heterotetrameric unit, with the interfacial [4Fe4S] cluster serving as a structural component toward the integrity of the heterodimeric structure to drive efficient catalysis.
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Affiliation(s)
- Benjamin R Duffus
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Marcel Gauglitz
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Teutloff
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Silke Leimkühler
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
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3
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Oliveira AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA. An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat Chem Biol 2024; 20:111-119. [PMID: 37985883 DOI: 10.1038/s41589-023-01484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vincent Fourmond
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Kateryna Klymanska
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Christophe Léger
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Bruno Guigliarelli
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Maia LB, Maiti BK, Moura I, Moura JJG. Selenium-More than Just a Fortuitous Sulfur Substitute in Redox Biology. Molecules 2023; 29:120. [PMID: 38202704 PMCID: PMC10779653 DOI: 10.3390/molecules29010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Living organisms use selenium mainly in the form of selenocysteine in the active site of oxidoreductases. Here, selenium's unique chemistry is believed to modulate the reaction mechanism and enhance the catalytic efficiency of specific enzymes in ways not achievable with a sulfur-containing cysteine. However, despite the fact that selenium/sulfur have different physicochemical properties, several selenoproteins have fully functional cysteine-containing homologues and some organisms do not use selenocysteine at all. In this review, selected selenocysteine-containing proteins will be discussed to showcase both situations: (i) selenium as an obligatory element for the protein's physiological function, and (ii) selenium presenting no clear advantage over sulfur (functional proteins with either selenium or sulfur). Selenium's physiological roles in antioxidant defence (to maintain cellular redox status/hinder oxidative stress), hormone metabolism, DNA synthesis, and repair (maintain genetic stability) will be also highlighted, as well as selenium's role in human health. Formate dehydrogenases, hydrogenases, glutathione peroxidases, thioredoxin reductases, and iodothyronine deiodinases will be herein featured.
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Affiliation(s)
- Luisa B. Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - Biplab K. Maiti
- Department of Chemistry, School of Sciences, Cluster University of Jammu, Canal Road, Jammu 180001, India
| | - Isabel Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - José J. G. Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
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5
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Kalimuthu P, Hakopian S, Niks D, Hille R, Bernhardt PV. The Reversible Electrochemical Interconversion of Formate and CO 2 by Formate Dehydrogenase from Cupriavidus necator. J Phys Chem B 2023; 127:8382-8392. [PMID: 37728992 DOI: 10.1021/acs.jpcb.3c04652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The bacterial molybdenum (Mo)-containing formate dehydrogenase (FdsDABG) from Cupriavidus necator is a soluble NAD+-dependent enzyme belonging to the DMSO reductase family. The holoenzyme is complex and possesses nine redox-active cofactors including a bis(molybdopterin guanine dinucleotide) (bis-MGD) active site, seven iron-sulfur clusters, and 1 equiv of flavin mononucleotide (FMN). FdsDABG catalyzes the two-electron oxidation of HCOO- (formate) to CO2 and reversibly reduces CO2 to HCOO- under physiological conditions close to its thermodynamic redox potential. Here we develop an electrocatalytically active formate oxidation/CO2 reduction system by immobilizing FdsDABG on a glassy carbon electrode in the presence of coadsorbents such as chitosan and glutaraldehyde. The reversible enzymatic interconversion between HCOO- and CO2 by FdsDABG has been realized with cyclic voltammetry using a range of artificial electron transfer mediators, with methylene blue (MB) and phenazine methosulfate (PMS) being particularly effective as electron acceptors for FdsDABG in formate oxidation. Methyl viologen (MV) acts as both an electron acceptor (MV2+) in formate oxidation and an electron donor (MV+•) for CO2 reduction. The catalytic voltammetry was reproduced by electrochemical simulation across a range of sweep rates and concentrations of formate and mediators to provide new insights into the kinetics of the FdsDABG catalytic mechanism.
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Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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6
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Kobayashi A, Taketa M, Sowa K, Kano K, Higuchi Y, Ogata H. Structure and function relationship of formate dehydrogenases: an overview of recent progress. IUCRJ 2023; 10:544-554. [PMID: 37668215 PMCID: PMC10478512 DOI: 10.1107/s2052252523006437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/24/2023] [Indexed: 09/06/2023]
Abstract
Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.
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Affiliation(s)
- Ami Kobayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Midori Taketa
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
| | - Keisei Sowa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kenji Kano
- Office of Society Academia Collaboration for Innovation, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hideaki Ogata
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
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7
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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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8
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The Mechanism of Metal-Containing Formate Dehydrogenases Revisited: The Formation of Bicarbonate as Product Intermediate Provides Evidence for an Oxygen Atom Transfer Mechanism. Molecules 2023; 28:molecules28041537. [PMID: 36838526 PMCID: PMC9962302 DOI: 10.3390/molecules28041537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Mo/W-containing formate dehydrogenases (FDH) catalyzed the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active sites. While in the reaction of formate oxidation, the product is CO2, which exits the active site via a hydrophobic channel; bicarbonate is formed as the first intermediate during the reaction at the active site. Other than what has been previously reported, bicarbonate is formed after an oxygen atom transfer reaction, transferring the oxygen from water to formate and a subsequent proton-coupled electron transfer or hydride transfer reaction involving the sulfido ligand as acceptor.
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9
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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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10
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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11
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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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12
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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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13
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Kirk ML, Hille R. Spectroscopic Studies of Mononuclear Molybdenum Enzyme Centers. Molecules 2022; 27:molecules27154802. [PMID: 35956757 PMCID: PMC9370002 DOI: 10.3390/molecules27154802] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
A concise review is provided of the contributions that various spectroscopic methods have made to our understanding of the physical and electronic structures of mononuclear molybdenum enzymes. Contributions to our understanding of the structure and function of each of the major families of these enzymes is considered, providing a perspective on how spectroscopy has impacted the field.
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Affiliation(s)
- Martin L. Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Correspondence: (M.L.K.); (R.H.)
| | - Russ Hille
- Department of Biochemistry, Boyce Hall 1463, University of California, Riverside, CA 82521, USA
- Correspondence: (M.L.K.); (R.H.)
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14
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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: 49] [Impact Index Per Article: 24.5] [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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15
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Nazemi A, Steeves AH, Kastner DW, Kulik HJ. Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase. J Phys Chem B 2022; 126:4069-4079. [PMID: 35609244 DOI: 10.1021/acs.jpcb.2c02260] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Mo/W-containing metalloenzyme formate dehydrogenase (FDH) is an efficient and selective natural catalyst that reversibly converts CO2 to formate under ambient conditions. In this study, we investigate the impact of the greater protein environment on the electrostatic potential (ESP) of the active site. To model the enzyme environment, we used a combination of classical molecular dynamics and multiscale quantum-mechanical (QM)/molecular-mechanical (MM) simulations. We leverage charge shift analysis to systematically construct QM regions and analyze the electronic environment of the active site by evaluating the degree of charge transfer between the core active site and the protein environment. The contribution of the terminal chalcogen ligand to the ESP of the metal center is substantial and dependent on the chalcogen identity, with similar, less negative ESPs for Se and S terminal chalcogens in comparison to O regardless of whether the metal is Mo or W. The orientation of the side chains and conformations of the cofactor also affect the ESP, highlighting the importance of sampling dynamic fluctuations in the protein. Overall, our observations suggest that the terminal chalcogen ligand identity plays an important role in the enzymatic activity of FDH, suggesting opportunities for a rational bioinspired catalyst design.
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Affiliation(s)
- Azadeh Nazemi
- Department of Chemical Engineering, 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
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Biological 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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16
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Hille R, Niks D. Application of EPR and related methods to molybdenum-containing enzymes. Methods Enzymol 2022; 666:373-412. [PMID: 35465925 DOI: 10.1016/bs.mie.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A description is provided of the contributions made to our understanding of molybdenum-containing enzymes through the application of electron paramagnetic resonance spectroscopy and related methods, by way of illustrating how these can be applied to better understand enzyme structure and function. An emphasis is placed on the use of EPR to identify both the coordination environment of the molybdenum coordination sphere as well as the structures of paramagnetic intermediates observed transiently in the course of reaction that have led to the elucidation of reaction mechanism.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, CA, United States.
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA, United States
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17
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Hakopian S, Niks D, Hille R. The air-inactivation of formate dehydrogenase FdsDABG from Cupriavidus necator. J Inorg Biochem 2022; 231:111788. [DOI: 10.1016/j.jinorgbio.2022.111788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 11/15/2022]
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18
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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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19
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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20
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Arias-Cartin R, Uzel A, Seduk F, Gerbaud G, Pierrel F, Broc M, Lebrun R, Guigliarelli B, Magalon A, Grimaldi S, Walburger A. Identification and characterization of a non-canonical menaquinone-linked formate dehydrogenase. J Biol Chem 2021; 298:101384. [PMID: 34748728 PMCID: PMC8808070 DOI: 10.1016/j.jbc.2021.101384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 10/25/2022] Open
Abstract
The Molybdenum/Tungsten-bispyranopterin guanine dinucleotides (Mo/W-bisPGD) family of Formate Dehydrogenases (FDHs) plays roles in several metabolic pathways ranging from carbon fixation to energy harvesting owing to their reaction with a wide variety of redox partners. Indeed, this metabolic plasticity results from the diverse structures, cofactor content, and substrates employed by partner subunits interacting with the catalytic hub. Here, we unveiled two non-canonical FDHs in Bacillus subtilis which are organized into two-subunit complexes with unique features, ForCE1 and ForCE2. We show that the ForC catalytic subunit interacts with an unprecedented partner subunit, ForE, and that its amino acid sequence within the active site deviates from the consensus residues typically associated with FDH activity, as a histidine residue is naturally substituted with a glutamine. The ForE essential subunit mediates the utilization of menaquinone as an electron acceptor as shown by the formate:menadione oxidoreductase activity of both enzymes, their copurification with menaquinone, and the distinctive detection of a protein-bound neutral menasemiquinone radical by multifrequency electron paramagnetic resonance (EPR) experiments on the purified enzymes. Moreover, EPR characterization of both FDHs reveals the presence of several [Fe-S] clusters with distinct relaxation properties and a weakly anisotropic Mo(V) EPR signature, consistent with the characteristic Mo/bisPGD cofactor of this enzyme family. Altogether, this work enlarges our knowledge of the FDH family by identifying a non-canonical FDH, which differs in terms of architecture, amino acid conservation around the Mo cofactor, and reactivity.
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Affiliation(s)
- Rodrigo Arias-Cartin
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France; Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France.
| | - Alexandre Uzel
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France
| | - Farida Seduk
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France
| | - Fabien Pierrel
- Grenoble Alpes Université, CNRS, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Marianne Broc
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France
| | - Régine Lebrun
- Aix Marseille Université, CNRS, Plateforme Protéomique de l'IMM, IM2B Marseille Protéomique (MaP), 13009 Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France
| | - Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France
| | - Stéphane Grimaldi
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France.
| | - Anne Walburger
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France.
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21
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Sproules S. Oxo versus Sulfido Coordination at Tungsten: A Spectroscopic and Correlated Ab Initio Electronic Structure Study. Inorg Chem 2021; 60:9057-9063. [PMID: 34096284 DOI: 10.1021/acs.inorgchem.1c01055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tungsten ion that resides at the active site of a unique class of enzymes only found in esoteric hyperthermophilic archaea bacteria is known to possess at least one terminal chalcogenide ligand. The identity of this as either an oxo or sulfido (or both) is difficult to ascertain from structural studies; therefore, small-molecule analogues are developed to calibrate and substantiate spectroscopic signatures obtained from native proteins. The electronic structures of Tp*WECl2 (E = O, S; Tp* = hydrotris(3,5-dimethylpyrazol-1-yl)borate) have been scrutinized using electronic, electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy to assess the impact of terminal chalcogen on the adjacent cis chloride ligands. Examination at the Cl K-edge provides a direct probe of the bonding and therein lability of these chloride ligands, and in conjunction with density functional theoretical and multireference calculations reveals greater bond covalency in Tp*WOCl2 compared to Tp*WSCl2. The computational model and electronic structure assignment are corroborated by the reproduction of spin-Hamiltonian parameters, whose magnitude is dominated by the sizeable spin-orbit coupling of tungsten.
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Affiliation(s)
- Stephen Sproules
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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22
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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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23
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Hossain MK, Plutenko MO, Schachner JA, Haukka M, Mösch-Zanetti NC, Fritsky IO, Nordlander E. Dioxomolybdenum(VI) complexes of hydrazone phenolate ligands - syntheses and activities in catalytic oxidation reactions. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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24
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Moon M, Park GW, Lee JP, Lee JS, Min K. Recent progress in formate dehydrogenase (FDH) as a non-photosynthetic CO2 utilizing enzyme: A short review. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Mintmier B, McGarry JM, Bain DJ, Basu P. Kinetic consequences of the endogenous ligand to molybdenum in the DMSO reductase family: a case study with periplasmic nitrate reductase. J Biol Inorg Chem 2020; 26:13-28. [PMID: 33131003 DOI: 10.1007/s00775-020-01833-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/20/2020] [Indexed: 11/24/2022]
Abstract
The molybdopterin enzyme family catalyzes a variety of substrates and plays a critical role in the cycling of carbon, nitrogen, arsenic, and selenium. The dimethyl sulfoxide reductase (DMSOR) subfamily is the most diverse family of molybdopterin enzymes and the members of this family catalyze a myriad of reactions that are important in microbial life processes. Enzymes in the DMSOR family can transform multiple substrates; however, quantitative information about the substrate preference is sparse, and, more importantly, the reasons for the substrate selectivity are not clear. Molybdenum coordination has long been proposed to impact the catalytic activity of the enzyme. Specifically, the molybdenum-coordinating residue may tune substrate preference. As such, molybdopterin enzyme periplasmic nitrate reductase (Nap) is utilized as a vehicle to understand the substrate preference and delineate the kinetic underpinning of the differences imposed by exchanging the molybdenum ligands. To this end, NapA from Campylobacter jejuni has been heterologously overexpressed, and a series of variants, where the molybdenum coordinating cysteine has been replaced with another amino acid, has been produced. The kinetic properties of these variants are discussed and compared with those of the native enzyme, providing quantitative information to understand the function of the molybdenum-coordinating residue.
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Affiliation(s)
- Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN, 46202, USA
| | - Jennifer M McGarry
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN, 46202, USA
| | - Daniel J Bain
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN, 46202, USA.
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26
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Robinson WE, Bassegoda A, Blaza JN, Reisner E, Hirst J. Understanding How the Rate of C-H Bond Cleavage Affects Formate Oxidation Catalysis by a Mo-Dependent Formate Dehydrogenase. J Am Chem Soc 2020; 142:12226-12236. [PMID: 32551568 PMCID: PMC7366381 DOI: 10.1021/jacs.0c03574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-dependent formate dehydrogenases (FDHs) catalyze the reversible conversion of formate into CO2, a proton, and two electrons. Kinetic studies of FDHs provide key insights into their mechanism of catalysis, relevant as a guide for the development of efficient electrocatalysts for formate oxidation as well as for CO2 capture and utilization. Here, we identify and explain the kinetic isotope effect (KIE) observed for the oxidation of formate and deuterioformate by the Mo-containing FDH from Escherichia coli using three different techniques: steady-state solution kinetic assays, protein film electrochemistry (PFE), and pre-steady-state stopped-flow methods. For each technique, the Mo center of FDH is reoxidized at a different rate following formate oxidation, significantly affecting the observed kinetic behavior and providing three different viewpoints on the KIE. Steady-state turnover in solution, using an artificial electron acceptor, is kinetically limited by diffusional intermolecular electron transfer, masking the KIE. In contrast, interfacial electron transfer in PFE is fast, lifting the electron-transfer rate limitation and manifesting a KIE of 2.44. Pre-steady-state analyses using stopped-flow spectroscopy revealed a KIE of 3 that can be assigned to the C-H bond cleavage step during formate oxidation. We formalize our understanding of FDH catalysis by fitting all the data to a single kinetic model, recreating the condition-dependent shift in rate-limitation of FDH catalysis between active-site chemical catalysis and regenerative electron transfer. Furthermore, our model predicts the steady-state and time-dependent concentrations of catalytic intermediates, providing a valuable framework for the design of future mechanistic experiments.
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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, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
| | - James N Blaza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters 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, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
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Radon C, Mittelstädt G, Duffus BR, Bürger J, Hartmann T, Mielke T, Teutloff C, Leimkühler S, Wendler P. Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase. Nat Commun 2020; 11:1912. [PMID: 32313256 PMCID: PMC7171172 DOI: 10.1038/s41467-020-15614-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/19/2020] [Indexed: 11/09/2022] Open
Abstract
Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load. Rhodobacter capsulatus NAD+ dependent formate dehydrogenase (RcFDH) is a molybdoenzyme that catalyses the reversible oxidation of formate to carbon dioxide, and is of interest for biotechnological applications. Here the authors present the cryo-EM structures of RcFDH as isolated from R. capsulatus and in the reduced state with bound NADH, and discuss the enzyme mechanism.
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Affiliation(s)
- Christin Radon
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Gerd Mittelstädt
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany.,Ferrier Research Institute, Victoria University of Wellington, Kelburn Parade, Wellington, 6012, New Zealand
| | - Benjamin R Duffus
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Jörg Bürger
- Max-Planck Institute of Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany.,Charité, Institut für Medizinische Physik und Biophysik, Charitéplatz 1, 10117, Berlin, Germany
| | - Tobias Hartmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Thorsten Mielke
- Max-Planck Institute of Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany.
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Functional mononuclear molybdenum enzymes: challenges and triumphs in molecular cloning, expression, and isolation. J Biol Inorg Chem 2020; 25:547-569. [PMID: 32279136 DOI: 10.1007/s00775-020-01787-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
Mononuclear molybdenum enzymes catalyze a variety of reactions that are essential in the cycling of nitrogen, carbon, arsenic, and sulfur. For decades, the structure and function of these crucial enzymes have been investigated to develop a fundamental knowledge for this vast family of enzymes and the chemistries they carry out. Therefore, obtaining abundant quantities of active enzyme is necessary for exploring this family's biochemical capability. This mini-review summarizes the methods for overexpressing mononuclear molybdenum enzymes in the context of the challenges encountered in the process. Effective methods for molybdenum cofactor synthesis and incorporation, optimization of expression conditions, improving isolation of active vs. inactive enzyme, incorporation of additional prosthetic groups, and inclusion of redox enzyme maturation protein chaperones are discussed in relation to the current molybdenum enzyme literature. This article summarizes the heterologous and homologous expression studies providing underlying patterns and potential future directions.
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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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30
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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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31
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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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Reschke S, Duffus BR, Schrapers P, Mebs S, Teutloff C, Dau H, Haumann M, Leimkühler S. Identification of YdhV as the First Molybdoenzyme Binding a Bis-Mo-MPT Cofactor in Escherichia coli. Biochemistry 2019; 58:2228-2242. [PMID: 30945846 DOI: 10.1021/acs.biochem.9b00078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The oxidoreductase YdhV in Escherichia coli has been predicted to belong to the family of molybdenum/tungsten cofactor (Moco/Wco)-containing enzymes. In this study, we characterized the YdhV protein in detail, which shares amino acid sequence homology with a tungsten-containing benzoyl-CoA reductase binding the bis-W-MPT (for metal-binding pterin) cofactor. The cofactor was identified to be of a bis-Mo-MPT type with no guanine nucleotides present, which represents a form of Moco that has not been found previously in any molybdoenzyme. Our studies showed that YdhV has a preference for bis-Mo-MPT over bis-W-MPT to be inserted into the enzyme. In-depth characterization of YdhV by X-ray absorption and electron paramagnetic resonance spectroscopies revealed that the bis-Mo-MPT cofactor in YdhV is redox active. The bis-Mo-MPT and bis-W-MPT cofactors include metal centers that bind the four sulfurs from the two dithiolene groups in addition to a cysteine and likely a sulfido ligand. The unexpected presence of a bis-Mo-MPT cofactor opens an additional route for cofactor biosynthesis in E. coli and expands the canon of the structurally highly versatile molybdenum and tungsten cofactors.
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Affiliation(s)
- Stefan Reschke
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
| | - Benjamin R Duffus
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
| | | | | | - Christian Teutloff
- Institute of Experimental Physics, EPR Spectroscopy of Biological Systems , Freie Universität Berlin , Arnimallee 14 , 14195 Berlin , Germany
| | | | | | - Silke Leimkühler
- Institute of Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Strasse 24 , 14476 Potsdam , Germany
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33
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Niks D, Hille R. Molybdenum- and tungsten-containing formate dehydrogenases and formylmethanofuran dehydrogenases: Structure, mechanism, and cofactor insertion. Protein Sci 2019; 28:111-122. [PMID: 30120799 PMCID: PMC6295890 DOI: 10.1002/pro.3498] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022]
Abstract
An overview is provided of the molybdenum- and tungsten-containing enzymes that catalyze the interconversion of formate and CO2 , focusing on common structural and mechanistic themes, as well as a consideration of the manner in which the mature Mo- or W-containing cofactor is inserted into apoprotein.
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Affiliation(s)
- Dimitri Niks
- Department of BiochemistryUniversity of CaliforniaRiverside
| | - Russ Hille
- Department of BiochemistryUniversity of CaliforniaRiverside
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34
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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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35
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Abstract
Two factors, climate change brought on by rising atmospheric CO2 levels and the accelerating shift toward renewable energy sources, have together worked to heighten interest in understanding how biological catalysts so effectively bring about the reduction of CO2 to formate, with potential applications for both bioremediation and energy storage. Most metal-dependent formate dehydrogenases, containing either molybdenum or tungsten in their active sites, function physiologically in the direction of formate oxidation to CO2, but it has become clear that many, if not all, are also effective in catalyzing the reverse reaction. In this chapter, we describe methods for isolating and characterizing these enzymes.
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Affiliation(s)
- Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, CA, United States.
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36
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Schwanhold N, Iobbi-Nivol C, Lehmann A, Leimkühler S. Same but different: Comparison of two system-specific molecular chaperones for the maturation of formate dehydrogenases. PLoS One 2018; 13:e0201935. [PMID: 30444874 PMCID: PMC6239281 DOI: 10.1371/journal.pone.0201935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022] Open
Abstract
The maturation of bacterial molybdoenzymes is a complex process leading to the insertion of the bulky bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor into the apo-enzyme. Most molybdoenzymes were shown to contain a specific chaperone for the insertion of the bis-MGD cofactor. Formate dehydrogenases (FDH) together with their molecular chaperone partner seem to display an exception to this specificity rule, since the chaperone FdhD has been proven to be involved in the maturation of all three FDH enzymes present in Escherichia coli. Multiple roles have been suggested for FdhD-like chaperones in the past, including the involvement in a sulfur transfer reaction from the l-cysteine desulfurase IscS to bis-MGD by the action of two cysteine residues present in a conserved CXXC motif of the chaperones. However, in this study we show by phylogenetic analyses that the CXXC motif is not conserved among FdhD-like chaperones. We compared in detail the FdhD-like homologues from Rhodobacter capsulatus and E. coli and show that their roles in the maturation of FDH enzymes from different subgroups can be exchanged. We reveal that bis-MGD-binding is a common characteristic of FdhD-like proteins and that the cofactor is bound with a sulfido-ligand at the molybdenum atom to the chaperone. Generally, we reveal that the cysteine residues in the motif CXXC of the chaperone are not essential for the production of active FDH enzymes.
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Affiliation(s)
- Nadine Schwanhold
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | | | - Angelika Lehmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
- * E-mail:
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37
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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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38
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Çakar MM, Mangas-Sanchez J, Birmingham WR, Turner NJ, Binay B. Discovery of a new metal and NAD +-dependent formate dehydrogenase from Clostridium ljungdahlii. Prep Biochem Biotechnol 2018; 48:327-334. [PMID: 29504829 DOI: 10.1080/10826068.2018.1446150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Over the next decades, with the growing concern of rising atmospheric carbon dioxide (CO2) levels, the importance of investigating new approaches for its reduction becomes crucial. Reclamation of CO2 for conversion into biofuels represents an alternative and attractive production method that has been studied in recent years, now with enzymatic methods gaining more attention. Formate dehydrogenases (FDHs) are NAD(P)H-dependent oxidoreductases that catalyze the conversion of formate into CO2 and have been extensively used for cofactor recycling in chemoenzymatic processes. A new FDH from Clostridium ljungdahlii (ClFDH) has been recently shown to possess activity in the reverse reaction: the mineralization of CO2 into formate. In this study, we show the successful homologous expression of ClFDH in Escherichia coli. Biochemical and kinetic characterization of the enzyme revealed that this homologue also demonstrates activity toward CO2 reduction. Structural analysis of the enzyme through homology modeling is also presented.
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Affiliation(s)
- M Mervan Çakar
- a Department of Chemistry , Gebze Technical University , Gebze , Kocaeli , Turkey
| | | | | | - Nicholas J Turner
- b School of Chemistry & MIB , University of Manchester , Manchester , UK
| | - Barış Binay
- c Department of Bioengineering , Gebze Technical University , Gebze , Kocaeli , Turkey
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39
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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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40
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Kaufmann P, Duffus BR, Mitrova B, Iobbi-Nivol C, Teutloff C, Nimtz M, Jänsch L, Wollenberger U, Leimkühler S. Modulating the Molybdenum Coordination Sphere of Escherichia coli Trimethylamine N-Oxide Reductase. Biochemistry 2018; 57:1130-1143. [PMID: 29334455 DOI: 10.1021/acs.biochem.7b01108] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The well-studied enterobacterium Escherichia coli present in the human gut can reduce trimethylamine N-oxide (TMAO) to trimethylamine during anaerobic respiration. The TMAO reductase TorA is a monomeric, bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor-containing enzyme that belongs to the dimethyl sulfoxide reductase family of molybdoenzymes. We report on a system for the in vitro reconstitution of TorA with molybdenum cofactors (Moco) from different sources. Higher TMAO reductase activities for TorA were obtained when using Moco sources containing a sulfido ligand at the molybdenum atom. For the first time, we were able to isolate functional bis-MGD from Rhodobacter capsulatus formate dehydrogenase (FDH), which remained intact in its isolated state and after insertion into apo-TorA yielded a highly active enzyme. Combined characterizations of the reconstituted TorA enzymes by electron paramagnetic resonance spectroscopy and direct electrochemistry emphasize that TorA activity can be modified by changes in the Mo coordination sphere. The combination of these results together with studies of amino acid exchanges at the active site led us to propose a novel model for binding of the substrate to the molybdenum atom of TorA.
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Affiliation(s)
- Paul Kaufmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam , 14476 Potsdam, Germany
| | - Benjamin R Duffus
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam , 14476 Potsdam, Germany
| | - Biljana Mitrova
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam , 14476 Potsdam, Germany
| | | | - Christian Teutloff
- Institute for Experimental Physics, Free University of Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Manfred Nimtz
- Helmholtz Center for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Lothar Jänsch
- Helmholtz Center for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Ulla Wollenberger
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam , 14476 Potsdam, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam , 14476 Potsdam, Germany
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41
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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: 50] [Impact Index Per Article: 7.1] [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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42
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Reschke S, Mebs S, Sigfridsson-Clauss KGV, Kositzki R, Leimkühler S, Haumann M. Protonation and Sulfido versus Oxo Ligation Changes at the Molybdenum Cofactor in Xanthine Dehydrogenase (XDH) Variants Studied by X-ray Absorption Spectroscopy. Inorg Chem 2017; 56:2165-2176. [DOI: 10.1021/acs.inorgchem.6b02846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Stefan Reschke
- Institut für
Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, 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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43
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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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44
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Correia MAS, Otrelo-Cardoso AR, Schwuchow V, Sigfridsson Clauss KGV, Haumann M, Romão MJ, Leimkühler S, Santos-Silva T. The Escherichia coli Periplasmic Aldehyde Oxidoreductase Is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. ACS Chem Biol 2016; 11:2923-2935. [PMID: 27622978 DOI: 10.1021/acschembio.6b00572] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crystallized an unusual member of the family, the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli. This is the first example of an E. coli protein containing a molybdopterin-cytosine-dinucleotide cofactor and is the only heterotrimer of the XO family so far structurally characterized. The crystal structure revealed the presence of an unexpected [4Fe-4S] cluster, anchored to an additional 40 residues subdomain. According to phylogenetic analysis, proteins containing this cluster are widely spread in many bacteria phyla, putatively through repeated gene transfer events. The active site of PaoABC is highly exposed to the surface with no aromatic residues and an arginine (PaoC-R440) making a direct interaction with PaoC-E692, which acts as a base catalyst. In order to understand the importance of R440, kinetic assays were carried out, and the crystal structure of the PaoC-R440H variant was also determined.
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Affiliation(s)
- Márcia A. S. Correia
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Viola Schwuchow
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | | | - Michael Haumann
- Freie Universität Berlin, Fachbereich Physik, 14195 Berlin, Germany
| | - Maria João Romão
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Silke Leimkühler
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | - Teresa Santos-Silva
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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45
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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: 75] [Impact Index Per Article: 9.4] [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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46
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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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47
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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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48
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Niks D, Duvvuru J, Escalona M, Hille R. Spectroscopic and Kinetic Properties of the Molybdenum-containing, NAD+-dependent Formate Dehydrogenase from Ralstonia eutropha. J Biol Chem 2015; 291:1162-74. [PMID: 26553877 DOI: 10.1074/jbc.m115.688457] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 11/06/2022] Open
Abstract
We have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, NAD(+)-dependent FdsABG formate dehydrogenase from Ralstonia eutropha. We confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). We have also characterized the electron paramagnetic resonance signal of the molybdenum center in its Mo(V) state and demonstrated the direct transfer of the substrate Cα hydrogen to the molybdenum center in the course of the reaction. Varying temperature, microwave power, and level of enzyme reduction, we are able to clearly identify the electron paramagnetic resonance signals for four of the iron/sulfur clusters of the enzyme and find suggestive evidence for two others; we observe a magnetic interaction between the molybdenum center and one of the iron/sulfur centers, permitting assignment of this signal to a specific iron/sulfur cluster in the enzyme. In light of recent advances in our understanding of the structure of the molybdenum center, we propose a reaction mechanism involving direct hydride transfer from formate to a molybdenum-sulfur group of the molybdenum center.
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Affiliation(s)
- Dimitri Niks
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
| | - Jayant Duvvuru
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
| | - Miguel Escalona
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
| | - Russ Hille
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
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