4UPE

Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.

Volbeda, A.Martin, L.Barbier, E.Gutierrez-Sanz, O.De Lacey, A.L.Liebgott, P.P.Dementin, S.Rousset, M.Fontecilla-Camps, J.C.

(2015) J. Biol. Inorg. Chem. 20: 11-22

  • DOI: 10.1007/s00775-014-1203-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because parti ...

    Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.


    Related Citations: 
    • 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.J.,Garcin, E.,Rousset, M.,Fontecilla-Camps, J.C.
      (2005) J.Biol.Inorg.Chem. 10: 239


    Organizational Affiliation

    University Grenoble Alpes, IBS, 38044, Grenoble, France, anne.volbeda@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NIFE-HYDROGENASE SMALL SUBUNIT
A, B, C
265Desulfovibrio 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
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
Q, R, S
548Desulfovibrio fructosivoransMutation(s): 1 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P18188 (Desulfovibrio fructosivorans)
Go to UniProtKB:  P18188
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A, B, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PO4
Query on PO4

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Q, R
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
F3S
Query on F3S

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

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Download CCD File 
Q, R, S
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Q, R, S
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Q, R, S
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Q, R, S
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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S
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
Q, R, S
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.430α = 90.00
b = 98.960β = 91.19
c = 184.950γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2015-01-21
    Type: Database references
  • Version 2.0: 2019-01-30
    Type: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation
  • Version 2.1: 2019-02-27
    Type: Data collection, Derived calculations, Experimental preparation