E.coli cofactor-dependent phosphoglycerate mutase complexed with vanadate

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.213 
  • R-Value Observed: 0.155 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1006/jmbi.2002.5418
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOGLYCERATE MUTASE249Escherichia coli K-12Mutation(s): 0 
Gene Names: PGM1
Find proteins for P62707 (Escherichia coli (strain K12))
Explore P62707 
Go to UniProtKB:  P62707
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62707
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.213 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.249α = 90
b = 112.142β = 90
c = 40.948γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Advisory, Data collection, Other, Refinement description
  • Version 1.4: 2023-12-13
    Changes: Advisory, Data collection, Database references, Other, Refinement description