4UCX

Structure of the T18G small subunit mutant of D. fructosovorans NiFe- hydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A threonine stabilizes the NiC and NiR catalytic intermediates of [NiFe]-hydrogenase.

Abou-Hamdan, A.Ceccaldi, P.Lebrette, H.Gutierrez-Sanz, O.Richaud, P.Cournac, L.Guigliarelli, B.De Lacey, A.L.Leger, C.Volbeda, A.Burlat, B.Dementin, S.

(2015) J Biol Chem 290: 8550-8558

  • DOI: 10.1074/jbc.M114.630491
  • Primary Citation of Related Structures:  
    4UCQ, 4UCW, 4UCX

  • PubMed Abstract: 
  • The heterodimeric [NiFe] hydrogenase from Desulfovibrio fructosovorans catalyzes the reversible oxidation of H2 into protons and electrons. The catalytic intermediates have been attributed to forms of the active site (NiSI, NiR, and NiC) detected using spectroscopic methods under potentiometric but non-catalytic conditions ...

    The heterodimeric [NiFe] hydrogenase from Desulfovibrio fructosovorans catalyzes the reversible oxidation of H2 into protons and electrons. The catalytic intermediates have been attributed to forms of the active site (NiSI, NiR, and NiC) detected using spectroscopic methods under potentiometric but non-catalytic conditions. Here, we produced variants by replacing the conserved Thr-18 residue in the small subunit with Ser, Val, Gln, Gly, or Asp, and we analyzed the effects of these mutations on the kinetic (H2 oxidation, H2 production, and H/D exchange), spectroscopic (IR, EPR), and structural properties of the enzyme. The mutations disrupt the H-bond network in the crystals and have a strong effect on H2 oxidation and H2 production turnover rates. However, the absence of correlation between activity and rate of H/D exchange in the series of variants suggests that the alcoholic group of Thr-18 is not necessarily a proton relay. Instead, the correlation between H2 oxidation and production activity and the detection of the NiC species in reduced samples confirms that NiC is a catalytic intermediate and suggests that Thr-18 is important to stabilize the local protein structure of the active site ensuring fast NiSI-NiC-NiR interconversions during H2 oxidation/production.


    Organizational Affiliation

    From the Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, UMR 7281 Aix-Marseille Université/CNRS, 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France, dementin@imm.cnrs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROGENASE (NIFE) SMALL SUBUNIT HYDAA, B, C264Desulfovibrio fructosivoransMutation(s): 1 
Gene Names: hydA
EC: 1.12.2.1
UniProt
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 SUBUNITD [auth Q], E [auth R], F [auth S]563Desulfovibrio fructosivoransMutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
UniProt
Find proteins for P18188 (Desulfovibrio fructosivorans)
Explore P18188 
Go to UniProtKB:  P18188
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth A], I [auth A], M [auth B], O [auth B], P [auth C], R [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
H [auth A], N [auth B], Q [auth C]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
DA [auth S], S [auth Q], Z [auth R]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth R] , GA [auth S] , HA [auth S] , J [auth A] , K [auth A] , L [auth A] , W [auth Q] , X [auth Q] , 
CA [auth R], GA [auth S], HA [auth S], J [auth A], K [auth A], L [auth A], W [auth Q], X [auth Q], Y [auth Q]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth R], EA [auth S], T [auth Q]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth R], FA [auth S], U [auth Q], V [auth Q]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.6α = 90
b = 99.27β = 92.32
c = 182.08γ = 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: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2019-01-30
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.4: 2019-11-20
    Changes: Derived calculations, Other