1B0P

CRYSTAL STRUCTURE OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.

Chabriere, E.Charon, M.H.Volbeda, A.Pieulle, L.Hatchikian, E.C.Fontecilla-Camps, J.C.

(1999) Nat.Struct.Mol.Biol. 6: 182-190

  • DOI: 10.1038/5870
  • Primary Citation of Related Structures:  2PDA

  • PubMed Abstract: 
  • Oxidative decarboxylation of pyruvate to form acetyl-coenzyme A, a crucial step in many metabolic pathways, is carried out in most aerobic organisms by the multienzyme complex pyruvate dehydrogenase. In most anaerobes, the same reaction is usually ca ...

    Oxidative decarboxylation of pyruvate to form acetyl-coenzyme A, a crucial step in many metabolic pathways, is carried out in most aerobic organisms by the multienzyme complex pyruvate dehydrogenase. In most anaerobes, the same reaction is usually catalyzed by a single enzyme, pyruvate:ferredoxin oxidoreductase (PFOR). Thus, PFOR is a potential target for drug design against certain anaerobic pathogens. Here, we report the crystal structures of the homodimeric Desulfovibrio africanus PFOR (data to 2.3 A resolution), and of its complex with pyruvate (3.0 A resolution). The structures show that each subunit consists of seven domains, one of which affords protection against oxygen. The thiamin pyrophosphate (TPP) cofactor and the three [4Fe-4S] clusters are suitably arranged to provide a plausible electron transfer pathway. In addition, the PFOR-pyruvate complex structure shows the noncovalent fixation of the substrate before the catalytic reaction.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of the Pyruvate- Ferredoxin Oxidoreductase from Desulfovibrio Africanus
      Pieulle, L.,Chabriere, E.,Hatchikian, E.C.,Fontecilla-Camps, J.F.,Charon, M.H.
      (1999) Acta Crystallogr.,Sect.D 55: 329


    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallogénèse des Protéines, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)
A, B
1231Desulfovibrio africanusGene Names: por
EC: 1.2.7.1
Find proteins for P94692 (Desulfovibrio africanus)
Go to UniProtKB:  P94692
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.800α = 90.00
b = 144.900β = 90.00
c = 203.000γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
CCP4data scaling
X-PLORrefinement
CCP4data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-23
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance