1H2A

SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history


Literature

Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis.

Higuchi, Y.Yagi, T.Yasuoka, N.

(1997) Structure 5: 1671-1680

  • DOI: https://doi.org/10.1016/s0969-2126(97)00313-4
  • Primary Citation of Related Structures:  
    1H2A

  • PubMed Abstract: 

    The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase. The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center. From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.


  • Organizational Affiliation

    Division of Chemistry, Graduate School of Science, Kyoto University, Japan. higuchi@kuchem.kyoto-u.ac.jp


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYDROGENASEA [auth S]317Nitratidesulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P21853 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21853 
Go to UniProtKB:  P21853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21853
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HYDROGENASEB [auth L]567Nitratidesulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P21852 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21852 
Go to UniProtKB:  P21852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21852
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.5α = 90
b = 126.5β = 90
c = 66.51γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
FSCALEdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other