4UQP

High-resolution structure of the D. fructosovorans NiFe-hydrogenase L122A mutant after exposure to air


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.Dementin, S.Rousset, M.Fontecilla-Camps, J.C.

(2015) J.Biol.Inorg.Chem. 20: 11

  • 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
PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
A, B
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
PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
Q, R
563Desulfovibrio fructosivoransMutation(s): 1 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P18188 (Desulfovibrio fructosivorans)
Go to UniProtKB:  P18188
Small Molecules
Ligands 9 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

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

Download SDF File 
Download CCD File 
Q, R
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
FCO
Query on FCO

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

Download SDF File 
Download CCD File 
B
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, Q, R
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SOT
Query on SOT

Download SDF File 
Download CCD File 
B
morpholine-4-sulfonic acid
C4 H9 N O4 S
GLGNSAPAWZUDRT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
Q, R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
Q, R
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
Q, R
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSS
Query on CSS
Q, R
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.120 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.700α = 90.00
b = 100.900β = 105.90
c = 116.700γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

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 1.2: 2019-02-27
    Type: Data collection, Derived calculations, Experimental preparation, Other