1H2R

THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.2 of the entry. See complete history


Literature

Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.

Higuchi, Y.Ogata, H.Miki, K.Yasuoka, N.Yagi, T.

(1999) Structure 7: 549-556

  • DOI: 10.1016/s0969-2126(99)80071-9
  • Primary Citation of Related Structures:  
    1H2R

  • PubMed Abstract: 
  • The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase ...

    The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase.


    Related Citations: 
    • Liberation of Hydrogen Sulfide During the Catalytic Action of Desulfoviborio Hydrogenase Under the Atmosphere of Hydrogen
      Higuchi, Y., Yagi, T.
      (1999) Biochem Biophys Res Commun 255: 295
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT) S267Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydADvMF_0271
EC: 1.12.2.1
Find proteins for P21853 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Explore P21853 
Go to UniProtKB:  P21853
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT) L534Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydBDvMF_0270
EC: 1.12.2.1
Find proteins for P21852 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Explore P21852 
Go to UniProtKB:  P21852
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
S
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NFE
Query on NFE

Download Ideal Coordinates CCD File 
L
NI-FE ACTIVE CENTER
C2 H Fe Ni O3 S2
BWHVFYQLNHWUMU-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.44α = 90
b = 126.86β = 90
c = 66.68γ = 90
Software Package:
Software NamePurpose
PROTEINmodel building
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
PROTEINphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1999-06-14 
  • Released Date: 2000-01-05 
  • Deposition Author(s): Higuchi, Y., Ogata, H.

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-05
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance