4UQL

High-resolution structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 

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:  
    4UPE, 4UQL, 4UPV, 4URH, 4UQP

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROGENASE (NIFE) SMALL SUBUNIT HYDAA, B265Desulfovibrio fructosivoransMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P18187 (Desulfovibrio fructosivorans)
Explore P18187 
Go to UniProtKB:  P18187
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNITC [auth Q], D [auth R]563Desulfovibrio fructosivoransMutation(s): 1 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P18188 (Desulfovibrio fructosivorans)
Explore P18188 
Go to UniProtKB:  P18188
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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F [auth A], L [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
SOT
Query on SOT

Download Ideal Coordinates CCD File 
N [auth B]morpholine-4-sulfonic acid
C4 H9 N O4 S
GLGNSAPAWZUDRT-UHFFFAOYSA-N
 Ligand Interaction
FCO
Query on FCO

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T [auth Q], Z [auth R]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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CA [auth R] , DA [auth R] , EA [auth R] , FA [auth R] , GA [auth R] , H [auth A] , I [auth A] , O [auth B] , 
CA [auth R],  DA [auth R],  EA [auth R],  FA [auth R],  GA [auth R],  H [auth A],  I [auth A],  O [auth B],  P [auth B],  R [auth B],  W [auth Q]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

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J [auth B], S [auth Q], Y [auth R]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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AA [auth R], U [auth Q]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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X [auth Q]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
H2S
Query on H2S

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Q [auth B]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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BA [auth R], V [auth Q]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
C [auth Q], D [auth R]L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
CSX
Query on CSX
C [auth Q], D [auth R]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.69α = 90
b = 100.85β = 105.96
c = 116.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2019-02-27
    Changes: Data collection, Derived calculations, Experimental preparation, Other