The Crystal Structure of the [NiFe] Hydrogenase from the Photosynthetic Bacterium Allochromatium vinosum: Characterization of the Oxidized Enzyme (Ni-A State)

Ogata, Hideaki; Kellers, Petra; Lubitz, Wolfgang

doi:10.1016/j.jmb.2010.07.041

Cited by 118 publications

(120 citation statements)

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“…The FT of the EXAFS spectrum of the MBH preparation preferentially in the in Ni ia -S state (pH 8.0) revealed largely diminished amplitudes, a shift of the main peak to larger distances, and a smaller peak feature due to short Ni-oxygen bonds compared to Ni-B ( Modified FeS clusters were also observed in crystal structures of standard H 2 ases, but mainly attributed to protein damage due to crystallization and/or X-ray induced modifications during data collection (93)(94). The presence of a special cluster also in the most native, membrane-containing preparation (43), the absence of X-ray induced damage under our XAS conditions, and similar Fe-XAS data for various protein samples argue against unspecific FeS cluster modifications in the MBH.…”

Section: Resultsmentioning

confidence: 99%

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

et al. 2011

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Molecular features that allow certain [NiFe] hydrogenases to catalyze the conversion of molecular hydrogen (H2) in the presence of dioxygen (O2) were investigated. Using X-ray absorption spectroscopy (XAS), we compared the [NiFe] active site and FeS clusters in the O2-tolerant membrane-bound hydrogenase (MBH) of Ralstonia eutropha and the O2-sensitive periplasmic hydrogenase (PH) of Desulfovibrio gigas. Fe-XAS indicated an unusual complement of iron–sulfur centers in the MBH, likely based on a specific structure of the FeS cluster proximal to the active site. This cluster is a [4Fe4S] cubane in PH. For MBH, it comprises less than ~2.7 Å Fe–Fe distances and additional longer vectors of ≥3.4 Å, consistent with an Fe trimer with a more isolated Fe ion. Ni-XAS indicated a similar architecture of the [NiFe] site in MBH and PH, featuring Ni coordination by four thiolates of conserved cysteines, i.e., in the fully reduced state (Ni-SR). For oxidized states, short Ni−μO bonds due to Ni–Fe bridging oxygen species were detected in the Ni-B state of the MBH and in the Ni-A state of the PH. Furthermore, a bridging sulfenate (CysSO) is suggested for an inactive state (Niia-S) of the MBH. We propose that the O2 tolerance of the MBH is mainly based on a dedicated electron donation from a modified proximal FeS cluster to the active site, which may favor formation of the rapidly reactivated Ni-B state instead of the slowly reactivated Ni-A state. Thereby, the catalytic activity of the MBH is facilitated in the presence of both H2 and O2.

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Section: Resultsmentioning

confidence: 99%

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

et al. 2011

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“…DsrM is a membrane-spanning b-type cytochrome, DsrK is an iron-sulfur protein resembling heterodisulfide reductase from methanogenic archaea (35). The Alvin_2037 and Alvin_2038 proteins are not copurifed with the A. vinosum Hyn [NiFe] hydrogenase (36). The observed transcriptional response of the complete hyn cluster to the presence of sulfide may point to a Data are compiled for genes for which transcription levels decreased at least 5-fold on one sulfur source or at least 2-fold on all tested sulfur sources; the average fold change for the corresponding microarray ratio(s) is highlighted in bold.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

Weißgerber

Dobler

Polen

et al. 2013

Journal of Bacteriology

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bThe purple sulfur bacterium Allochromatium vinosum DSM 180 T is one of the best-studied sulfur-oxidizing anoxygenic phototrophic bacteria, and it has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organism's high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur, or sulfite compared to photoorganoheterotrophic growth on malate. Differential expression of 1,178 genes was observed, corresponding to 30% of the A. vinosum genome. Relative transcription of 551 genes increased significantly during growth on one of the different sulfur sources, while the relative transcript abundance of 627 genes decreased. A significant number of genes that revealed strongly enhanced relative transcription levels have documented sulfur metabolism-related functions. Among these are the dsr genes, including dsrAB for dissimilatory sulfite reductase, and the sgp genes for the proteins of the sulfur globule envelope, thus confirming former results. In addition, we identified new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Those four genes for hypothetical proteins that exhibited the strongest increases of mRNA levels on sulfide and elemental sulfur, respectively, were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for sulfur globule formation during the oxidation of sulfide and thiosulfate and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria.

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“…In the Desulfovibrio fructosovorans hydrogenase crystal structure corresponding to the Ni-B form a (hydr)oxo ligand bridges the Ni and the Fe ions of the active site (8). Conversely, in the oxidized as-isolated structure, we modeled the Ni-A state with a diatomic [NiFe] bridging ligand that we assigned as (hydro)-peroxo (8); however, such assignment has not been universally accepted (9). It appears that the formation of either Ni-A or Ni-B states depends on the number of electrons, either two or four, that can rapidly react with O 2 at the active site upon air exposure (10).…”

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X-ray crystallographic and computational studies of the O ₂ -tolerant [NiFe]-hydrogenase 1 from Escherichia coli

Volbeda

Amara

Darnault

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

192

269

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The crystal structure of the membrane-bound O 2 -tolerant [NiFe]-hydrogenase 1 from Escherichia coli (EcHyd-1) has been solved in three different states: as-isolated, H 2 -reduced, and chemically oxidized. As very recently reported for similar enzymes from Ralstonia eutropha and Hydrogenovibrio marinus, two supernumerary Cys residues coordinate the proximal [FeS] cluster in EcHyd-1, which lacks one of the inorganic sulfide ligands. We find that the as-isolated, aerobically purified species contains a mixture of at least two conformations for one of the cluster iron ions and Glu76. In one of them, Glu76 and the iron occupy positions that are similar to those found in O 2 -sensitive [NiFe]-hydrogenases. In the other conformation, this iron binds, besides three sulfur ligands, the amide N from Cys20 and one Oϵ of Glu76. Our calculations show that oxidation of this unique iron generates the high-potential form of the proximal cluster. The structural rearrangement caused by oxidation is confirmed by our H 2 -reduced and oxidized EcHyd-1 structures. Thus, thanks to the peculiar coordination of the unique iron, the proximal cluster can contribute two successive electrons to secure complete reduction of O 2 to H 2 O at the active site. The two observed conformations of Glu76 are consistent with this residue playing the role of a base to deprotonate the amide moiety of Cys20 upon iron binding and transfer the resulting proton away, thus allowing the second oxidation to be electroneutral. The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O 2 reduction, located near the active site.[4Fe-3S] cluster | membrane-bound hydrogenase | Mössbauer spectroscopy | QM/MM | structure/function relationships

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The Crystal Structure of the [NiFe] Hydrogenase from the Photosynthetic Bacterium Allochromatium vinosum: Characterization of the Oxidized Enzyme (Ni-A State)

Cited by 118 publications

References 70 publications

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

X-ray crystallographic and computational studies of the O ₂ -tolerant [NiFe]-hydrogenase 1 from Escherichia coli

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The Crystal Structure of the [NiFe] Hydrogenase from the Photosynthetic Bacterium Allochromatium vinosum: Characterization of the Oxidized Enzyme (Ni-A State)

Cited by 118 publications

References 70 publications

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O2-Tolerant H2 Cleavage

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O2-Tolerant H2 Cleavage

Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

X-ray crystallographic and computational studies of the O 2 -tolerant [NiFe]-hydrogenase 1 from Escherichia coli

Contact Info

Product

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[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

X-ray crystallographic and computational studies of the O ₂ -tolerant [NiFe]-hydrogenase 1 from Escherichia coli