2C3P

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


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:  
    2C3M, 2C3O, 2C3P, 2C3U, 2C3Y, 2C42, 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 obtained snapshots of unreacted and partially reacted (probably as a tetrahedral intermediate) pyruvate-PFOR complexes at different time intervals ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE-FERREDOXIN OXIDOREDUCTASEA, B1,231Desulfocurvibacter 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1TP
Query on 1TP

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
1-(2-{(2S,4R,5R)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-[(1S)-1-CARBOXY-1-HYDROXYETHYL]-4-METHYL-1,3-THIAZOLIDIN-5-YL}ETHOXY)-1,1,3,3-TETRAHYDROXY-1LAMBDA~5~-DIPHOSPHOX-1-EN-2-IUM 3-OXIDE
C15 H26 N4 O10 P2 S
TYOXZTVUMWOHPA-JPRMETQZSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.966α = 90
b = 145.84β = 90
c = 210.822γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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