1YRQ

Structure of the ready oxidized form of [NiFe]-hydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.

Volbeda, A.Martin, L.Cavazza, C.Matho, M.Faber, B.W.Roseboom, W.Albracht, S.P.Garcin, E.Rousset, M.Fontecilla-Camps, J.C.

(2005) J.Biol.Inorg.Chem. 10: 239-249

  • DOI: 10.1007/s00775-005-0632-x
  • Primary Citation of Related Structures:  
  • Also Cited By: 4URH, 4UQP, 4UQL, 4UPV, 4UPE, 3CUS, 3CUR

  • PubMed Abstract: 
  • [NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis ...

    [NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.


    Related Citations: 
    • Gas access to the active site of Ni-Fe hydrogenase probed by X-ray crystallography and molecular dynamics
      Montet, Y.,Amara, P.,Volbeda, A.,Vernede, X.,Hatchikian, E.C.,Field, M.J.,Frey, M.,Fontecilla-Camps, J.C.
      (1997) Nat.Struct.Mol.Biol. 4: 523
    • High-resolution crystallographic analysis of Desulfovibrio fructosovorans [NiFe] hydrogenase
      Volbeda, A.,Montet, Y.,Vernede, X.,Hatchikian, E.C.,Fontecilla-Camps, J.C.
      (2002) Int.J.Hydrogen Energy 27: 1449


    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallogenèse des Protèines, Institut de Biologie Structurale J.P. Ebel (CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027, Grenoble Cédex 1, France. anne.volbeda@ibs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase small subunit
A, B, C, D, F, G
264Desulfovibrio fructosivoransMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P18187 (Desulfovibrio fructosivorans)
Go to UniProtKB:  P18187
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase large subunit
H, I, J, K, M, N
549Desulfovibrio fructosivoransMutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P18188 (Desulfovibrio fructosivorans)
Go to UniProtKB:  P18188
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C, D, F, G
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
A, B, C, D, F, G
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download SDF File 
Download CCD File 
H, I, J, K, M, N
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
H, I, J, K, M, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
H, I, J, K, M, N
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 127.500α = 90.00
b = 99.700β = 91.80
c = 183.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
ProDCdata collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description