1FRF

CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

Starting Model: experimental
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This is version 3.1 of the entry. See complete history


Literature

3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis

Rousset, M.Montet, Y.Guigliarelli, B.Forget, N.Asso, M.Bertrand, P.Fontecilla-Camps, J.C.Hatchikian, E.C.

(1998) Proc Natl Acad Sci U S A 95: 11625-11630

  • DOI: https://doi.org/10.1073/pnas.95.20.11625
  • Primary Citation of Related Structures:  
    1FRF

  • PubMed Abstract: 

    The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed.


  • Organizational Affiliation

    Unité de Bioénergétique et Ingéniérie des Protéines, Institut de Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique, 31, Chemin Joseph Aiguier, 13402 Marseille CDX 20, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[NI-FE] HYDROGENASEA [auth S]264Solidesulfovibrio fructosivoransMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
[NI-FE] HYDROGENASEB [auth L]564Solidesulfovibrio fructosivoransMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth S],
E [auth S]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
D [auth S]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
G [auth L]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
F [auth L]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.61α = 90
b = 99.77β = 90.88
c = 184.51γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
CCP4data reduction
AMoREphasing
X-PLORrefinement
XDSdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-07-29
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2018-04-04
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2018-04-11
    Changes: Data collection
  • Version 3.0: 2023-08-09
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.1: 2024-11-06
    Changes: Structure summary