1KEK | pdb_00001kek

Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.227 (Depositor) 
  • R-Value Work: 
    0.178 (Depositor) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase.

Chabriere, E.Vernede, X.Guigliarelli, B.Charon, M.H.Hatchikian, E.C.Fontecilla-Camps, J.C.

(2001) Science 294: 2559-2563

  • DOI: https://doi.org/10.1126/science.1066198
  • Primary Citation Related Structures: 
    1KEK

  • PubMed Abstract: 

    In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.


  • Organizational Affiliation
    • Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, Université Joseph Fourier, CNRS, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

Macromolecule Content 

  • Total Structure Weight: 270.67 kDa 
  • Atom Count: 20,775 
  • 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
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HTL

Query on HTL



Download:Ideal Coordinates CCD File
H [auth A],
O [auth B]
2-ACETYL-THIAMINE DIPHOSPHATE
C14 H21 N4 O8 P2 S
GYRGKLZCJRVYRV-UHFFFAOYSA-O
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-UHFFFAOYSA-N
CO2

Query on CO2



Download:Ideal Coordinates CCD File
I [auth A],
P [auth B]
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
CA

Query on CA



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

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.227 (Depositor) 
  • R-Value Work:  0.178 (Depositor) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.11α = 90
b = 145.76β = 90
c = 210.26γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLORrefinement
REFMACrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary