Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 270.67 kDa 
• Atom Count: 18894 
• Modelled Residue Count: 2462 
• Deposited Residue Count: 2462 
• Unique protein chains: 1

2PDA

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

• DOI: 10.2210/pdb2PDA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfocurvibacter africanus
• Mutation(s): No 


• Deposited: 1998-11-10 Released: 1999-04-23 
• Deposition Author(s): Chabriere, E., Charon, M.H.

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Experimental Data Snapshot

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

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

• PubMed: 10048931 
• DOI: 10.1038/5870
• Primary Citation of Related Structures:  
  2PDA, 1B0P


• 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). 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)	A, B	1231	Desulfocurvibacter africanus	Mutation(s): 0  Gene Names: por EC: 1.2.7.1
UniProt
Find proteins for P94692 (Desulfocurvibacter africanus) Explore P94692  Go to UniProtKB:  P94692

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	H [auth A], O [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4	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
PYR	I [auth A], P [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
CA	D [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	C [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 86	α = 90
b = 146.3	β = 90
c = 211.9	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-11-10 
• Released Date: 1999-04-23 
Deposition Author(s): Chabriere, E., Charon, M.H.

Revision History  

• 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