2C3Y

CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate.

Cavazza, C.Contreras-Martel, C.Pieulle, L.Chabriere, E.Hatchikian, E.C.Fontecilla-Camps, J.C.

(2006) Structure 14: 217

  • DOI: 10.1016/j.str.2005.10.013
  • Primary Citation of Related Structures:  
  • Also Cited By: 2UZA

  • PubMed Abstract: 
  • Pyruvate-ferredoxin oxidoreductases (PFOR) are unique among thiamine pyrophosphate (ThDP)-containing enzymes in giving rise to a rather stable cofactor-based free-radical species upon the decarboxylation of their first substrate, pyruvate. We have ob ...

    Pyruvate-ferredoxin oxidoreductases (PFOR) are unique among thiamine pyrophosphate (ThDP)-containing enzymes in giving rise to a rather stable cofactor-based free-radical species upon the decarboxylation of their first substrate, pyruvate. We have obtained snapshots of unreacted and partially reacted (probably as a tetrahedral intermediate) pyruvate-PFOR complexes at different time intervals. We conclude that pyruvate decarboxylation involves very limited substrate-to-product movements but a significant displacement of the thiazolium moiety of ThDP. In this respect, PFOR seems to differ substantially from other ThDP-containing enzymes, such as transketolase and pyruvate decarboxylase. In addition, exposure of PFOR to oxygen in the presence of pyruvate results in significant inhibition of catalytic activity, both in solution and in the crystals. Examination of the crystal structure of inhibited PFOR suggests that the loss of activity results from oxime formation at the 4' amino substituent of the pyrimidine moiety of ThDP.


    Related Citations: 
    • 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 2559: 294


    Organizational Affiliation

    Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, UJF, CNRS, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE-FERREDOXIN OXIDOREDUCTASE
A, B
1231Desulfovibrio africanusMutation(s): 0 
Gene Names: por
EC: 1.2.7.1
Find proteins for P94692 (Desulfovibrio africanus)
Go to UniProtKB:  P94692
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HTL
Query on HTL

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A, B
2-ACETYL-THIAMINE DIPHOSPHATE
2-ACETYL-3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-4-METHYL-5-(4,6,6-TRIHYDROXY-3,5-DIOXA-4,6-DIPHOSPHAHEX-1-YL)THIAZOLIUM INNER SALT P,P'-DIOXIDE
C14 H21 N4 O8 P2 S
GYRGKLZCJRVYRV-UHFFFAOYSA-O
 Ligand Interaction
CO2
Query on CO2

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Download CCD File 
A, B
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.081α = 90.00
b = 145.639β = 90.00
c = 211.619γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-15
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance