Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.32 kDa 
• Atom Count: 4185 
• Residue Count: 508 
• Unique protein chains: 1

1EJJ

CRYSTAL STRUCTURAL ANALYSIS OF PHOSPHOGLYCERATE MUTASE COCRYSTALLIZED WITH 3-PHOSPHOGLYCERATE

• DOI: 10.2210/pdb1EJJ/pdb

• Classification: ISOMERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2000-03-02 Released: 2001-03-02 
• Deposition Author(s): Jedrzejas, M.J., Chander, M., Setlow, P., Krishnasamy, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.247 
• R-Value Work: 0.207 

Literature

Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus.

Jedrzejas, M.J., Chander, M., Setlow, P., Krishnasamy, G.

(2000) EMBO J 19: 1419-1431

• PubMed: 10747010 
• DOI: 10.1093/emboj/19.7.1419
• Primary Citation of Related Structures:  
  1EJJ


• PubMed Abstract: 
  

Bacillus stearothermophilus phosphoglycerate mutase (PGM), which interconverts 2- and 3-phosphoglyceric acid (PGA), does not require 2,3-diphosphoglyceric acid for activity. However, this enzyme does have an absolute and specific requirement for Mn(2+) ions for catalysis. Here we report the crystal structure of this enzyme complexed with 3PGA and manganese ions to 1.9 A resolution; this is the first crystal structure of a diphosphoglycerate-independent PGM to be determined. This information, plus the location of the two bound Mn(2+) ions and the 3PGA have allowed formulation of a possible catalytic mechanism for this PGM. In this mechanism Mn(2+) ions facilitate the transfer of the substrate's phosphate group to Ser62 to form a phosphoserine intermediate. In the subsequent phosphotransferase part of the reaction, the phosphate group is transferred from Ser62 to the O2 or O3 positions of the reoriented glycerate to yield the PGA product. Site-directed mutagenesis studies were used to confirm our mechanism and the involvement of specific enzyme residues in Mn(2+) binding and catalysis.

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Organizational Affiliation: 

Department of Microbiology, University of Alabama at Birmingham, 933 19th Street South, Birmingham, AL 35294, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOGLYCERATE MUTASE	A	511	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: gpmI, pgm EC: 5.4.2.1 (PDB Primary Data), 5.4.2.12 (UniProt)
Find proteins for Q9X519 (Geobacillus stearothermophilus) Explore Q9X519  Go to UniProtKB:  Q9X519

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PG	A	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.247 
• R-Value Work: 0.207 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.486	α = 90
b = 206.293	β = 90
c = 125.134	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-02 
• Released Date: 2001-03-02 
Deposition Author(s): Jedrzejas, M.J., Chander, M., Setlow, P., Krishnasamy, G.

Revision History 

• Version 1.0: 2001-03-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance