Refinement of the nickel site structure in Desulfovibrio gigas hydrogenase using range-extended EXAFS spectroscopy

Gu, Weiwei; Jacquamet, Lilian; Patil, Daulat S.; Wang, H X; Evans, David; Smith, Matt C.; Millar, Michelle; Koch, Stephen A.; Eichhorn, David M.; Latimer, Matthew J.; Cramer, Stephen P.

doi:10.1016/s0162-0134(02)00494-4

Cited by 51 publications

(113 citation statements)

References 52 publications

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“…4A) of the PH in the Ni-A state revealed two main peaks due to Ni-oxygen and Ni-sulfur bonds. Features at higher distances reflected contributions from the Ni-Fe vector (23,60). The best-fit parameters (Table 3-I) showed that the Ni-A spectrum was completely described by close to one short Ni-oxygen distance, four Ni-sulfur bonds from the cysteines at the active site, and a Ni-Fe distance of 2.75 Å, all of which are similar to those found in crystal structures (50,53).…”

Section: Resultssupporting

confidence: 60%

[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: Resultssupporting

confidence: 60%

[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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“…To extend the EXAFS range beyond the Fe K-edge, we used the procedure described by Gu et al (2003). The K afluorescence predominantly resulting from Mn excitation (detection at approx.…”

Section: Results and Discussion (A) Extended-range Exafsmentioning

confidence: 99%

On the structure of the manganese complex of photosystem II: extended-range EXAFS data and specific atomic-resolution models for four S-states

Dau

Grundmeier

Loja

et al. 2007

Phil. Trans. R. Soc. B

172

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The water-oxidizing manganese complex bound to the proteins of photosystem II (PSII) was studied by X-ray absorption spectroscopy on PSII membrane particles. An extended range for collection of extended X-ray absorption fine-structure (EXAFS) data was used (up to 16.6 Å K1 ). The EXAFS suggests the presence of two Mn-Mn distances close to 2.7 Å (per Mn 4 Ca complex); the existence of a third Mn-Mn distance below 2.9 Å is at least uncertain. Interestingly, a distance of 3.7 Å is clearly resolved in the extended-range data and tentatively assigned to a Mn-Mn distance. Taking into account the above EXAFS results (inter alia), we present a model for the structure of the PSII manganese complex, which differs from previous atomic-resolution models. Emphasizing the hypothetical character, we propose for all semi-stable S-states: (i) a structure of the Mn 4 Ca(m-O) n core, (ii) a model of the amino acid environment, and (iii) assignments of distinct Mn oxidation states to all the individual Mn ions. This specific working model may permit discussion, verification and invalidation of its various features in comparison with experimental and theoretical findings.

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“…No long-range Ni····Fe interactions were found [76] and the original transform peaks attributed to these seem to be due to noise in the data. Thus, the crystallography was likely of a photo-reduced active site, and while the early EXAFS was wrong about the presence of long-range Ni····Fe, it correctly indicated a lack of short-range interactions.…”

Section: Photo-reduction Artifactsmentioning

confidence: 92%

“…showed that H 2 reduced enzyme had a short Ni····Fe contact but that oxidized enzyme did not [76]. No long-range Ni····Fe interactions were found [76] and the original transform peaks attributed to these seem to be due to noise in the data.…”

Section: Photo-reduction Artifactsmentioning

confidence: 96%

Metalloprotein active site structure determination: Synergy between X-ray absorption spectroscopy and X-ray crystallography

Cotelesage

Pushie

Grochulski

et al. 2012

Journal of Inorganic Biochemistry

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Refinement of the nickel site structure in Desulfovibrio gigas hydrogenase using range-extended EXAFS spectroscopy

Cited by 51 publications

References 52 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

On the structure of the manganese complex of photosystem II: extended-range EXAFS data and specific atomic-resolution models for four S-states

Metalloprotein active site structure determination: Synergy between X-ray absorption spectroscopy and X-ray crystallography

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Refinement of the nickel site structure in Desulfovibrio gigas hydrogenase using range-extended EXAFS spectroscopy

Cited by 51 publications

References 52 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

On the structure of the manganese complex of photosystem II: extended-range EXAFS data and specific atomic-resolution models for four S-states

Metalloprotein active site structure determination: Synergy between X-ray absorption spectroscopy and X-ray crystallography

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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