1B0P | pdb_00001b0p

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 (Depositor) 
  • R-Value Work: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1B0P

This is version 1.6 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: https://doi.org/10.1038/5870
  • Primary Citation 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). 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.


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

Macromolecule Content 

  • Total Structure Weight: 270.5 kDa 
  • Atom Count: 19,411 
  • Modeled Residue Count: 2,462 
  • Deposited Residue Count: 2,462 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)
A, B
1,231Desulfocurvibacter africanusMutation(s): 0 
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP

Query on TPP



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4

Query on SF4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.271 (Depositor) 
  • R-Value Work:  0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.8α = 90
b = 144.9β = 90
c = 203γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
CCP4data reduction
X-PLORrefinement
XDSdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2018-04-11
    Changes: Data collection
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.6: 2024-11-13
    Changes: Structure summary