3FOQ | pdb_00003foq

Crystal structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group.

• PDB DOI: https://doi.org/10.2210/pdb3FOQ/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-31 Released: 2009-06-09 
• Deposition Author(s): Verma, S.K., Prakash, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 
  0.321 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.285 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.287 (Depositor) 

Literature

Structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group.

Verma, S.K., Jaiswal, M., Kumar, N., Parikh, A., Nandicoori, V.K., Prakash, B.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 435-439

• PubMed: 19407371 
• DOI: https://doi.org/10.1107/S1744309109010252
• Primary Citation of Related Structures:  
  3FOQ


• PubMed Abstract: 
  

  GlmU is a bifunctional enzyme that catalyzes the final two steps in the biosynthesis of UDP-GlcNAc. Crystals of GlmU from Mycobacterium tuberculosis obtained using ammonium sulfate as a precipitant diffracted poorly (to 3.4 A resolution) and displayed an unusually high solvent content (>80%) with sparse crystal packing that resulted in large solvent channels. With one molecule per asymmetric unit, the monomers from three neighbouring asymmetric units related by the crystal threefold formed a biological trimer. Although this is the first report of the structure of GlmU determined in a cubic crystal form, the trimeric arrangement here is similar to that observed for other GlmU structures determined in hexagonal (H3, H32, P6(3)22) space groups.

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Organizational Affiliation: 

Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 53.11 kDa 
• Atom Count: 3,186 
• Modelled Residue Count: 439 
• Deposited Residue Count: 503 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein glmU	A	503	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: glmU, MRA_1026, MT1046, Rv1018c EC: 2.7.7.23 (PDB Primary Data), 2.3.1.157 (PDB Primary Data)
UniProt
Find proteins for P9WMN3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMN3  Go to UniProtKB:  P9WMN3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free:  0.321 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.285 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.287 (Depositor) 

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 285.7	α = 90
b = 285.7	β = 90
c = 285.7	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Verma, S.K., Prakash, B.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations