Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.57 kDa 
• Atom Count: 4327 
• Modelled Residue Count: 503 
• Deposited Residue Count: 513 
• Unique protein chains: 1

4MY4

Crystal structure of phosphoglycerate mutase from Staphylococcus aureus.

• PDB DOI: 10.2210/pdb4MY4/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-27 Released: 2013-10-16 
• Deposition Author(s): Roychowdhury, A., Kundu, A., Gujar, A., Bose, M., Das, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.216 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 

Literature

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

• PubMed: 25611430 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-independent phosphoglycerate mutase	A	513	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: gpmI, SAOUHSC_00798 EC: 5.4.2.1 (PDB Primary Data), 5.4.2.12 (UniProt)
UniProt
Find proteins for Q2G029 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G029  Go to UniProtKB:  Q2G029

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.216 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.206	α = 90
b = 81.747	β = 90
c = 89.184	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-27 
• Released Date: 2013-10-16 
Deposition Author(s): Roychowdhury, A., Kundu, A., Gujar, A., Bose, M., Das, A.K.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Database references
• Version 1.2: 2015-04-08
  Changes: Database references