1O98

1.4A CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights Into the Catalytic Mechanism of Cofactor-Independent Phosphoglycerate Mutase from X-Ray Crystallography, Simulated Dynamics and Molecular Modeling

Rigden, D.J.Mello, L.V.Lamani, E.Littlejohn, J.E.Jedrzejas, M.J.

(2003) J.Mol.Biol. 328: 909

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphoglycerate mutases catalyze the isomerization of 2 and 3-phosphoglycerates, and are essential for glucose metabolism in most organisms. Here, we further characterize the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Ba ...

    Phosphoglycerate mutases catalyze the isomerization of 2 and 3-phosphoglycerates, and are essential for glucose metabolism in most organisms. Here, we further characterize the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus by determination of a high-resolution (1.4A) crystal structure of the wild-type enzyme and the crystal structure of its S62A mutant. The mutant structure surprisingly showed the replacement of one of the two catalytically essential manganese ions with a water molecule, offering an additional possible explanation for its lack of catalytic activity. Crystal structures invariably show substrate phosphoglycerate to be entirely buried in a deep cleft between the two iPGM domains. Flexibility analyses were therefore employed to reveal the likely route of substrate access to the catalytic site through an aperture created in the enzyme's surface during certain stages of the catalytic process. Several conserved residues lining this aperture may contribute to orientation of the substrate as it enters. Factors responsible for the retention of glycerate within the phosphoenzyme structure in the proposed mechanism are identified by molecular modeling of the glycerate complex of the phosphoenzyme. Taken together, these results allow for a better understanding of the mechanism of action of iPGMs. Many of the results are relevant to a series of evolutionarily related enzymes. These studies will facilitate the development of iPGM inhibitors which, due to the demonstrated importance of this enzyme in many bacteria, would be of great potential clinical significance.


    Organizational Affiliation

    National Centre of Genetic Resources and Biotechnology, Cenargen/Embrapa, S.A.I.N. Parque Rural, Final W5, Asa Norte, 70770-900 Brasília, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE
A
511Geobacillus stearothermophilusMutation(s): 0 
Gene Names: gpmI (pgm)
EC: 5.4.2.12
Find proteins for Q9X519 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9X519
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
2PG
Query on 2PG

Download SDF File 
Download CCD File 
A
2-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
GXIURPTVHJPJLF-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 58.515α = 90.00
b = 205.787β = 90.00
c = 125.018γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance