Crystal structure of phosphopglycerate mutase from Staphylococcus aureus in 3-phosphoglyceric acid bound form.

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

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Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism

Roychowdhury, A.Kundu, A.Bose, M.Gujar, A.Mukherjee, S.Das, A.K.

(2015) FEBS J 282: 1097-1110

  • DOI: https://doi.org/10.1111/febs.13205
  • Primary Citation of Related Structures:  
    4MY4, 4NWJ, 4NWX

  • PubMed Abstract: 

    Cofactor-independent phosphoglycerate mutase (iPGM), an important enzyme in glycolysis and gluconeogenesis, catalyses the isomerization of 2- and 3-phosphoglycerates by an Mn(2+)-dependent phospho-transfer mechanism via a phospho-enzyme intermediate. Crystal structures of bi-domain iPGM from Staphylococcus aureus, together with substrate-bound forms, have revealed a new conformation of the enzyme, representing an intermediate state of domain movement. The substrate-binding site and the catalytic site are present in two distinct domains in the intermediate form. X-ray crystallography complemented by simulated dynamics has enabled delineation of the complete catalytic cycle, which includes binding of the substrate, followed by its positioning into the catalytic site, phospho-transfer and finally product release. The present work describes a novel mechanism of domain movement controlled by a hydrophobic patch that is exposed on domain closure and acts like a spring to keep the protein in open conformation. Domain closing occurs after substrate binding, and is essential for phospho-transfer, whereas the open conformation is a prerequisite for efficient substrate binding and product dissociation. A new model of catalysis has been proposed by correlating the hinge-bending motion with the phospho-transfer mechanism.

  • Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology, Kharagpur, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,3-bisphosphoglycerate-independent phosphoglycerate mutase513Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: gpmISAOUHSC_00798
Find proteins for Q2G029 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G029 
Go to UniProtKB:  Q2G029
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G029
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.637α = 90
b = 82.841β = 90
c = 89.145γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2015-04-08
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description