1YRQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 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: https://doi.org/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. 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.


  • 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase small subunit264Solidesulfovibrio fructosivoransMutation(s): 0 
EC: 1.12.2.1
UniProt
Find proteins for P18187 (Solidesulfovibrio fructosivorans)
Explore P18187 
Go to UniProtKB:  P18187
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18187
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase large subunit549Solidesulfovibrio fructosivoransMutation(s): 0 
EC: 1.12.2.1
UniProt
Find proteins for P18188 (Solidesulfovibrio fructosivorans)
Explore P18188 
Go to UniProtKB:  P18188
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18188
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth D]
GA [auth D]
KA [auth F]
M [auth A]
AA [auth C],
EA [auth D],
GA [auth D],
KA [auth F],
M [auth A],
MA [auth F],
O [auth A],
QA [auth G],
S [auth B],
SA [auth G],
U [auth B],
Y [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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FA [auth D]
LA [auth F]
N [auth A]
RA [auth G]
T [auth B]
FA [auth D],
LA [auth F],
N [auth A],
RA [auth G],
T [auth B],
Z [auth C]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FCO
Query on FCO

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DA [auth J]
JA [auth K]
PA [auth M]
R [auth H]
VA [auth N]
DA [auth J],
JA [auth K],
PA [auth M],
R [auth H],
VA [auth N],
X [auth I]
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI
Query on NI

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BA [auth J]
HA [auth K]
NA [auth M]
P [auth H]
TA [auth N]
BA [auth J],
HA [auth K],
NA [auth M],
P [auth H],
TA [auth N],
V [auth I]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MG
Query on MG

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CA [auth J]
IA [auth K]
OA [auth M]
Q [auth H]
UA [auth N]
CA [auth J],
IA [auth K],
OA [auth M],
Q [auth H],
UA [auth N],
W [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.5α = 90
b = 99.7β = 91.8
c = 183.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ProDCdata collection
XDSdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-23
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-12-06
    Changes: Data collection, Derived calculations
  • Version 1.6: 2024-10-09
    Changes: Structure summary