1E59

E.coli cofactor-dependent phosphoglycerate mutase complexed with vanadate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic Implications for Escherichia Coli Cofactor-Dependent Phosphoglycerate Mutase Based on the High-Resolution Crystal Structure of a Vanadate Complex.

Bond, C.S.White, M.Hunter, W.N.

(2002) J.Mol.Biol. 316: 1071

  • DOI: 10.1006/jmbi.2002.5418

  • PubMed Abstract: 
  • The structure of Escherichia coli cofactor-dependent phosphoglycerate mutase (dPGM), complexed with the potent inhibitor vanadate, has been determined to a resolution of 1.30 A (R-factor 0.159; R-free 0.213). The inhibitor is present in the active si ...

    The structure of Escherichia coli cofactor-dependent phosphoglycerate mutase (dPGM), complexed with the potent inhibitor vanadate, has been determined to a resolution of 1.30 A (R-factor 0.159; R-free 0.213). The inhibitor is present in the active site, principally as divanadate, but with evidence of additional vanadate moieties at either end, and representing a different binding mode to that observed in the structural homologue prostatic acid phosphatase. The analysis reveals the enzyme-ligand interactions involved in inhibition of the mutase activity by vanadate and identifies a water molecule, observed in the native E.coli dPGM structure which, once activated by vanadate, may dephosphorylate the active protein. Rather than reflecting the active conformation previously observed for E.coli dPGM, the inhibited protein's conformation resembles that of the inactive dephosphorylated Saccharomyces cerevisiae dPGM. The provision of a high-resolution structure of both active and inactive forms of dPGM from a single organism, in conjunction with computational modelling of substrate molecules in the active site provides insight into the binding of substrates and the specific interactions necessary for three different activities, mutase, synthase and phosphatase, within a single active site. The sequence similarity of E.coli and human dPGMs allows us to correlate structure with clinical pathology.


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOGLYCERATE MUTASE
A
249Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gpmA (gpm, pgm, pgmA)
EC: 5.4.2.11
Find proteins for P62707 (Escherichia coli (strain K12))
Go to UniProtKB:  P62707
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
VO3
Query on VO3

Download SDF File 
Download CCD File 
A
TETRAMETAVANADATE
O13 V4
JXIADNYSXBZKBU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.249α = 90.00
b = 112.142β = 90.00
c = 40.948γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-97refinement
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance