1YQ9

Structure of the unready oxidized form of [NiFe] hydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.132 

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: 
    • Crystal Structure of the nickel-iron hydrogenase from Desulfovibrio gigas
      Volbeda, A.,Charon, M.H.,Piras, C.,Hatchikian, E.C.,Frey, M.,Fontecilla-Camps, J.C.
      (1995) Nature 373: 580
    • Structure of the [NiFe] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands
      Volbeda, A.,Garcin, E.,Piras, C.,De Lacey, A.L.,Fernandez, V.M.,Hatchikian, E.C.,Frey, M.,Fontecilla-Camps, J.C.
      (1996) J.Am.Chem.Soc. 118: 12989


    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
264Desulfovibrio gigasMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P12943 (Desulfovibrio gigas)
Go to UniProtKB:  P12943
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase large subunit
H, I
536Desulfovibrio gigasMutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P12944 (Desulfovibrio gigas)
Go to UniProtKB:  P12944
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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Download CCD File 
A, B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

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Download CCD File 
H, I
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
H2S
Query on H2S

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Download CCD File 
A, B, H, I
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

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H, I
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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H, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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H, I
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.132 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 62.750α = 89.33
b = 93.440β = 102.41
c = 69.030γ = 90.95
Software Package:
Software NamePurpose
AMoREphasing
XDSdata scaling
ProDCdata collection
PDB_EXTRACTdata extraction
REFMACrefinement

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: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description