1WUK

High resolution Structure Of The Oxidized State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.094 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Activation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state

Hirota, S.Nakahara, A.Komori, H.Shibata, N.Kato, T.Kano, K.Higuchi, Y.Ogata, H.

(2005) Structure 13: 1635-1642

  • DOI: 10.1016/j.str.2005.07.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation ...

    Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready). We have succeeded in converting Ni-B to Ni-A with the use of Na2S and O2 and determining the high-resolution crystal structures of both states. Ni-B possesses a monatomic nonprotein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species. The terminal atom of the bridging species of Ni-A occupies a similar position as C of the exogenous CO in the CO complex (inhibited state). The common features of the enzyme structures at the unready (Ni-A) and inhibited (CO complex) states are proposed. These findings provide useful information on the design of new systems of biomimetic dihydrogen production and fuel cell devices.


    Organizational Affiliation

    Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Ako-gun, Hyogo 678-1297, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase small subunit
S
267Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P21853 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21853
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase large subunit
L
534Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P21852 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21852
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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Download CCD File 
S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
S
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NFO
Query on NFO

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Download CCD File 
L
NI-FE OXIDIZED ACTIVE CENTER
C3 H2 Fe N Ni O3
FQZPNHHVQDQMNS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
L
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.094 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.291α = 90.00
b = 125.843β = 90.00
c = 66.440γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXmodel building
CNSphasing
SHELXL-97refinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance