2PDA

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.234 

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 Biol 6: 182-190

  • DOI: 10.1038/5870
  • Primary Citation of Related Structures:  
    1B0P, 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 catalyzed by a single enzyme, pyruvate:ferredoxin oxidoreductase (PFOR) ...

    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 D Biol Crystallogr 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)A, B1231Desulfocurvibacter africanusMutation(s): 0 
Gene Names: por
EC: 1.2.7.1
UniProt
Find proteins for P94692 (Desulfocurvibacter africanus)
Explore P94692 
Go to UniProtKB:  P94692
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP94692
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP
Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]		THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
PYR
Query on PYR
Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]		PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86α = 90
b = 146.3β = 90
c = 211.9γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-23
    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