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Yang JY, Kerr TA, Wang XS, Barlow JM. Reducing CO2 to HCO2– at Mild Potentials: Lessons from Formate Dehydrogenase. J Am Chem Soc 2020; 142:19438-19445. [DOI: 10.1021/jacs.0c07965] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jenny Y. Yang
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Tyler A. Kerr
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Xinran S. Wang
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jeffrey M. Barlow
- Department of Chemistry, University of California, Irvine, California 92697, United States
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Abstract
Tungsten is the heaviest element used in biological systems. It occurs in the active sites of several bacterial or archaeal enzymes and is ligated to an organic cofactor (metallopterin or metal binding pterin; MPT) which is referred to as tungsten cofactor (Wco). Wco-containing enzymes are found in the dimethyl sulfoxide reductase (DMSOR) and the aldehyde:ferredoxin oxidoreductase (AOR) families of MPT-containing enzymes. Some depend on Wco, such as aldehyde oxidoreductases (AORs), class II benzoyl-CoA reductases (BCRs) and acetylene hydratases (AHs), whereas others may incorporate either Wco or molybdenum cofactor (Moco), such as formate dehydrogenases, formylmethanofuran dehydrogenases or nitrate reductases. The obligately tungsten-dependent enzymes catalyze rather unusual reactions such as ones with extremely low-potential electron transfers (AOR, BCR) or an unusual hydration reaction (AH). In recent years, insights into the structure and function of many tungstoenzymes have been obtained. Though specific and unspecific ABC transporter uptake systems have been described for tungstate and molybdate, only little is known about further discriminative steps in Moco and Wco biosynthesis. In bacteria producing Moco- and Wco-containing enzymes simultaneously, paralogous isoforms of the metal insertase MoeA may be specifically involved in the molybdenum- and tungsten-insertion into MPT, and in targeting Moco or Wco to their respective apo-enzymes. Wco-containing enzymes are of emerging biotechnological interest for a number of applications such as the biocatalytic reduction of CO2, carboxylic acids and aromatic compounds, or the conversion of acetylene to acetaldehyde.
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Zhang Y, Zheng J. Bioinformatics of Metalloproteins and Metalloproteomes. Molecules 2020; 25:molecules25153366. [PMID: 32722260 PMCID: PMC7435645 DOI: 10.3390/molecules25153366] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-755-2692-2024
| | - Junge Zheng
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
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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: 11] [Impact Index Per Article: 2.8] [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: 39] [Impact Index Per Article: 9.8] [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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56
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Kirk ML, Kc K. Molybdenum and Tungsten Cofactors and the Reactions They Catalyze. Met Ions Life Sci 2020; 20:/books/9783110589757/9783110589757-015/9783110589757-015.xml. [PMID: 32851830 PMCID: PMC8176780 DOI: 10.1515/9783110589757-015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The last 20 years have seen a dramatic increase in our mechanistic understanding of the reactions catalyzed by pyranopterin Mo and W enzymes. These enzymes possess a unique cofactor (Moco) that contains a novel ligand in bioinorganic chemistry, the pyranopterin ene-1,2-dithiolate. A synopsis of Moco biosynthesis and structure is presented, along with our current understanding of the role Moco plays in enzymatic catalysis. Oxygen atom transfer (OAT) reactivity is discussed in terms of breaking strong metal-oxo bonds and the mechanism of OAT catalyzed by enzymes of the sulfite oxidase (SO) family that possess dioxo Mo(VI) active sites. OAT reactivity is also discussed in members of the dimethyl sulfoxide (DMSO) reductase family, which possess des-oxo Mo(IV) sites. Finally, we reveal what is known about hydride transfer reactivity in xanthine oxidase (XO) family enzymes and the formate dehydrogenases. The formal hydride transfer reactivity catalyzed by xanthine oxidase family enzymes is complex and cleaves substrate C-H bonds using a mechanism that is distinct from monooxygenases. The chapter primarily highlights developments in the field that have occurred since ~2000, which have contributed to our collective structural and mechanistic understanding of the three canonical pyranopterin Mo enzymes families: XO, SO, and DMSO reductase.
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Laureanti JA, Ginovska B, Buchko GW, Schenter GK, Hebert M, Zadvornyy OA, Peters JW, Shaw WJ. A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO2 Hydrogenation. Organometallics 2020. [DOI: 10.1021/acs.organomet.9b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bojana Ginovska
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Gregory K. Schenter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Margaret Hebert
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - John W. Peters
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Wendy J. Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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58
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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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59
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Methanogenesis involves direct hydride transfer from H2 to an organic substrate. Nat Rev Chem 2020; 4:213-221. [PMID: 37128042 DOI: 10.1038/s41570-020-0167-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2020] [Indexed: 01/02/2023]
Abstract
Certain anaerobic microorganisms evolved a mechanism to use H2 as a reductant in their energy metabolisms. For these purposes, the microorganisms developed H2-activating enzymes, which are aspirational catalysts in a sustainable hydrogen economy. In the case of the hydrogenotrophic pathway performed by methanogenic archaea, 8e- are extracted from 4H2 and used as reducing equivalents to convert CO2 into CH4. Under standard cultivation conditions, these archaea express [NiFe]-hydrogenases, which are Ni-dependent and Fe-dependent enzymes and heterolytically cleave H2 into 2H+ and 2e-, the latter being supplied into the central metabolism. Under Ni-limiting conditions, F420-reducing [NiFe]-hydrogenases are downregulated and their functions are predominantly taken over by an upregulated [Fe]-hydrogenase. Unique in biology, this Fe-dependent hydrogenase cleaves H2 and directly transfers H- to an imidazolium-containing substrate. [Fe]-hydrogenase activates H2 at an Fe cofactor ligated by two CO molecules, an acyl group, a pyridinol N atom and a cysteine thiolate as the central constituent. This Fe centre has inspired chemists to not only design synthetic mimics to catalytically cleave H2 in solution but also for incorporation into apo-[Fe]-hydrogenase to give semi-synthetic proteins. This Perspective describes the enzymes involved in hydrogenotrophic methanogenesis, with a focus on those performing the reduction steps. Of these, we describe [Fe]-hydrogenases in detail and cover recent progress in their synthetic modelling.
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Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics. ISME JOURNAL 2020; 14:906-918. [PMID: 31896784 PMCID: PMC7082340 DOI: 10.1038/s41396-019-0571-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/20/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolates or enrichment cultures, but these may not reflect the true diversity and in situ activities of the syntrophs predominating in full-scale systems. Here we obtained 182 medium to high quality metagenome-assembled genomes (MAGs) from the microbiome of two full-scale anaerobic digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentrations of acetate, propionate, or butyrate, separately. The most pronounced response to butyrate was observed for two MAGs of the recently described genus Candidatus Phosphitivorax (phylum Desulfobacterota), expressing a butyrate beta-oxidation pathway. For propionate, the largest response was observed for an MAG of a novel genus in the family Pelotomaculaceae, transcribing a methylmalonyl-CoA pathway. All three species were common in anaerobic digesters at Danish wastewater treatment plants as shown by amplicon analysis, and this is the first time their syntrophic features involved in SCFA oxidation were revealed with transcriptomic evidence. Further, they also possessed unique genomic features undescribed in well-characterized syntrophs, including the metabolic pathways for phosphite oxidation, nitrite and sulfate reduction.
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61
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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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62
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Fernandes HS, Teixeira CSS, Sousa SF, Cerqueira NMFSA. Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:E2462. [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] [MESH Headings] [Grants] [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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Affiliation(s)
- Henrique S Fernandes
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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63
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Muras V, Toulouse C, Fritz G, Steuber J. Respiratory Membrane Protein Complexes Convert Chemical Energy. Subcell Biochem 2019; 92:301-335. [PMID: 31214991 DOI: 10.1007/978-3-030-18768-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The invention of a biological membrane which is used as energy storage system to drive the metabolism of a primordial, unicellular organism represents a key event in the evolution of life. The innovative, underlying principle of this key event is respiration. In respiration, a lipid bilayer with insulating properties is chosen as the site for catalysis of an exergonic redox reaction converting substrates offered from the environment, using the liberated Gibbs free energy (ΔG) for the build-up of an electrochemical H+ (proton motive force, PMF) or Na+ gradient (sodium motive force, SMF) across the lipid bilayer. Very frequently , several redox reactions are performed in a consecutive manner, with the first reaction delivering a product which is used as substrate for the second redox reaction, resulting in a respiratory chain. From today's perspective, the (mostly) unicellular bacteria and archaea seem to be much simpler and less evolved when compared to multicellular eukaryotes. However, they are overwhelmingly complex with regard to the various respiratory chains which permit survival in very different habitats of our planet, utilizing a plethora of substances to drive metabolism. This includes nitrogen, sulfur and carbon compounds which are oxidized or reduced by specialized, respiratory enzymes of bacteria and archaea which lie at the heart of the geochemical N, S and C-cycles. This chapter gives an overview of general principles of microbial respiration considering thermodynamic aspects, chemical reactions and kinetic restraints. The respiratory chains of Escherichia coli and Vibrio cholerae are discussed as models for PMF- versus SMF-generating processes, respectively. We introduce main redox cofactors of microbial respiratory enzymes, and the concept of intra-and interelectron transfer. Since oxygen is an electron acceptor used by many respiratory chains, the formation and removal of toxic oxygen radicals is described. Promising directions of future research are respiratory enzymes as novel bacterial targets, and biotechnological applications relying on respiratory complexes.
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Affiliation(s)
- Valentin Muras
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Charlotte Toulouse
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Günter Fritz
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
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