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 
  • R-Value Observed: 0.135 

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:  
    1YQ9, 1YQW, 1YRQ

  • 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 for this difference has not been understood because of lack of relevant crystallographic data ...

    [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: 
    • 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
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase small subunitA, C [auth B]264Desulfovibrio gigasMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
UniProt
Find proteins for P12943 (Desulfovibrio gigas)
Explore P12943 
Go to UniProtKB:  P12943
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase large subunitB [auth H], D [auth I]536Desulfovibrio gigasMutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
UniProt
Find proteins for P12944 (Desulfovibrio gigas)
Explore P12944 
Go to UniProtKB:  P12944
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth A], G [auth A], T [auth B], V [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
F [auth A], U [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
AA [auth I], O [auth H]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], L [auth A], R [auth H], S [auth H], X [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
M [auth H], Y [auth I]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
H2S
Query on H2S

Download Ideal Coordinates CCD File 
CA [auth I], H [auth A], Q [auth H], W [auth B]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

Download Ideal Coordinates CCD File 
BA [auth I], P [auth H]PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth H], Z [auth I]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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 
  • R-Value Observed: 0.135 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.75α = 89.33
b = 93.44β = 102.41
c = 69.03γ = 90.95
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
XDSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description