Molecular Basis of Proton Motive Force Generation: Structure of Formate Dehydrogenase-N

Jormakka, Mika; Törnroth, Susanna; Byrne, Bernadette; Iwata, So

doi:10.1126/science.1068186

Cited by 474 publications

(448 citation statements)

References 26 publications

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“…The coordination sphere of the molybdenum (or tungsten) center was completed with a sulfur atom, and a SeCH 3 group that was chosen to mimic the SeCys 140 residue. The model was subsequently completed with the conserved His 141 , Arg 333 , and Val 139 residues (amino acid numbering corresponding to E. coli Fdh-H) [4,6,7,12,13]. Conventional protonation states for all amino acids at pH 7 were adopted and the carboxylate and the amino groups of the terminal amino acids of each chain of the model were protonated.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

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The mechanism of formate oxidation by metal-dependent formate dehydrogenases

et al. 2011

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Metal-dependent formate dehydrogenases (Fdh) from prokaryotic organisms are members of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and tungsten-containing enzymes. Fdhs catalyze the oxidation of the formate anion to carbon dioxide in a redox reaction that involves the transfer of two electrons from the substrate to the active site. The active site in the oxidized state comprises a hexacoordinated molybdenum or tungsten ion in a distorted trigonal prismatic geometry. Using this structural model, we calculated the catalytic mechanism of Fdh through density functional theory tools. The simulated mechanism was correlated with the experimental kinetic properties of three different Fdhs isolated from three different Desulfovibrio species. Our studies indicate that the C-H bond break is an event involved in the rate-limiting step of the catalytic cycle. The role in catalysis of conserved amino acid residues involved in metal coordination and near the metal active site is discussed on the basis of experimental and theoretical results.

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Section: Theoretical Calculationsmentioning

confidence: 99%

“…The crystal structures of three of these enzymes have been reported. The molybdenumcontaining enzymes are Fdh-H and the membrane-bound Fdh-N from Escherichia coli K12 [4][5][6][7][8][9][10]. The tungstencontaining enzyme is the periplasmic Fdh from the sulfatereducing bacterium Desulfovibrio gigas [9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

et al. 2011

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“…The Mo-containing enzymes are the Fdh-H from Escherichia coli [17], which is one of the components of the formate hydrogen lyase complex in E. coli, and the recently reported membrane-bound Fdh-N from E. coli, which is supposed to participate in the redox loop of the proton motive force generation across the membrane cell [18]. The W-containing enzyme is the Fdh from the sulfate-reducing bacterium (SRB) Desulfovibrio gigas [19,20].…”

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confidence: 99%

“…The W-containing enzyme is the Fdh from the sulfate-reducing bacterium (SRB) Desulfovibrio gigas [19,20]. E. coli Fdh-H is a monomeric enzyme (79 kDa), while the E. coli Fdh-N is an abc heterotrimer with subunits of 113, 32, and 21 kDa, respectively [18]. The W-Fdh from D. gigas is a heterodimeric enzyme with 92 and 29 kDa subunits, respectively (Fig.…”

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confidence: 99%

Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases

et al. 2004

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Molybdenum and tungsten are second-and third-row transition elements, respectively, which are found in a mononuclear form in the active site of a diverse group of enzymes that generally catalyze oxygen atom transfer reactions. Mononuclear Mo-containing enzymes have been classified into three families: xanthine oxidase, DMSO reductase, and sulfite oxidase. The proteins of the DMSO reductase family present the widest diversity of properties among its members and our knowledge about this family was greatly broadened by the study of the enzymes nitrate reductase and formate dehydrogenase, obtained from different sources. We discuss in this review the information of the better characterized examples of these two types of Mo enzymes and W enzymes closely related to the members of the DMSO reductase family. We briefly summarize, also, the few cases reported so far for enzymes that can function either with Mo or W at their active site.

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“…Further analysis showed that these are more similar to cytochrome b561-like sequences as discussed below (section 3.5, Figure S5). (Berks et al, 1995, Jormakka et al, 2002.…”

Section: Cytochrome-b Of the B 6 F And The Bc Complexmentioning

confidence: 99%

Evolution of b-type cytochromes in prokaryotes

Koumandou

Κοσσίδα

2015

Preprint

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Abstract:Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b 6 f complex, ubiquinol and menaquinol reductases, formate dehydrogenase, Ni/Fehydrogenase, and succinate dehydrogenase). We use data from 272 species of fully sequenced bacteria and archaea, which represent the full diversity of prokaryotic lineages and multiple bioenergetic modes, to examine the distribution of these cytochromes across lineages, and ask the question of whether sequences from different species cluster by cytochrome-b family, by bioenergetic mode or by taxonomic group. Different cytochrome-b types are found in many lineages of the bacteria and archaea, and form distinct groups in phylogenetic analysis, which indicates an ancient origin for this complex, and diversification of different cytochrome-b types before the diversification of lineages. We find that species do not cluster based on bioenergetic mode. We also re-examine data from previous studies using this expanded sample of organisms spanning the full diversity of prokaryotic lineages. Concerning the b 6 f complex of photosynthetic organisms, our expanded phylogenies do not show significant bootstrap support for a "green clade" of cytochrome b 6 ; also, the split form of b 6 is not monophyletic, indicating that the split form arose independently multiple times. We also present data on the similarities between prokaryotic and eukaryotic cytochrome b561 sequences, in light of the recently reported structure of eukaryotic cytochrome b561.PeerJ PrePrints | https://doi.org/10.7287/peerj.preprints.1564v1 | CC-BY 4.0 Open Access |

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Molecular Basis of Proton Motive Force Generation: Structure of Formate Dehydrogenase-N

Cited by 474 publications

References 26 publications

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases

Evolution of b-type cytochromes in prokaryotes

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