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: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 2.2 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.P.Dementin, S.Rousset, M.Fontecilla-Camps, J.C.

(2015) J Biol Inorg Chem 20: 11-22

  • DOI: https://doi.org/10.1007/s00775-014-1203-9
  • Primary Citation of Related Structures:  
    4UPE, 4UPV, 4UQL, 4UQP, 4URH

  • 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. 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NIFE-HYDROGENASE SMALL SUBUNIT
A, B, C
265Solidesulfovibrio 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNITD [auth Q],
E [auth R],
F [auth S]
548Solidesulfovibrio fructosivoransMutation(s): 1 
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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth A]
I [auth A]
J [auth B]
L [auth B]
M [auth C]
G [auth A],
I [auth A],
J [auth B],
L [auth B],
M [auth C],
O [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
GA [auth S]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
FCO
Query on FCO

Download Ideal Coordinates CCD File 
CA [auth S],
P [auth Q],
V [auth R]
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth R],
U [auth Q]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth S],
S [auth Q],
T [auth Q],
Y [auth R],
Z [auth R]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
DA [auth S],
Q,
W [auth R]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth R],
EA [auth S],
R [auth Q],
X [auth R]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
D [auth Q],
E [auth R],
F [auth S]
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.43α = 90
b = 98.96β = 91.19
c = 184.95γ = 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 2.0: 2019-01-30
    Changes: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation
  • Version 2.1: 2019-02-27
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 2.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description