2WU8 | pdb_00002wu8

Structural studies of phosphoglucose isomerase from Mycobacterium tuberculosis H37Rv

• PDB DOI: https://doi.org/10.2210/pdb2WU8/pdb

• Classification: ISOMERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-01 Released: 2009-10-27 
• Deposition Author(s): Anand, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.223 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structural Studies of Phosphoglucose Isomerase from Mycobacterium Tuberculosis H37Rv

Anand, K., Mathur, D., Anant, A., Garg, L.C.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 490

• PubMed: 20445242 
• DOI: https://doi.org/10.1107/S1744309110011656
• Primary Citation Related Structures: 
  2WU8


• PubMed Abstract: 
  

  Phosphoglucose isomerase (PGI) plays a key role in both glycolysis and gluconeogenesis inside the cell, whereas outside the cell it exhibits cytokine properties. PGI is also known to act as an autocrine motility factor, a neuroleukin agent and a differentiation and maturation mediator. Here, the first crystal structure of PGI from Mycobacterium tuberculosis H37Rv (Mtb) is reported. The structure was refined at 2.25 A resolution and revealed the presence of one molecule in the asymmetric unit with two globular domains. As known previously, the active site of Mtb PGI contains conserved residues including Glu356, Glu216 and His387 (where His387 is from the neighbouring molecule). The crystal structure of Mtb PGI was observed to be rather more similar to human PGI than other nonbacterial PGIs, with only a few differences being detected in the loops, arm and hook regions of the human and Mtb PGIs, suggesting that the M. tuberculosis enzyme uses the same enzyme mechanism.

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Organizational Affiliation: 
• European Molecular Biology Laboratory Heidelberg, Structural and Computational Biology Unit, Meyerhof Strasse 1, D-69117 Heidelberg, Germany. [e-mail],[e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 59.78 kDa 
• Atom Count: 4,483 
• Modeled Residue Count: 549 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSE-6-PHOSPHATE ISOMERASE	A	549	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 5.3.1.9
UniProt
Find proteins for P9WN69 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN69  Go to UniProtKB:  P9WN69

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.223 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.7	α = 90
b = 118.5	β = 90
c = 137.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Anand, K.

Revision History  

• Version 1.0: 2009-10-27
  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: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description