4HCQ

Crystal structure of GLMU from mycobacterium tuberculosis in complex with glucosamine-1-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Crystal structures identify an atypical two-metal-ion mechanism for uridyltransfer in GlmU: its significance to sugar nucleotidyl transferases

Jagtap, P.K.A.Verma, S.K.Vithani, N.Bais, V.S.Prakash, B.

(2013) J Mol Biol 425: 1745-1759

  • DOI: https://doi.org/10.1016/j.jmb.2013.02.019
  • Primary Citation of Related Structures:  
    4G87, 4HCQ

  • PubMed Abstract: 

    N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU), exclusive to prokaryotes, is a bifunctional enzyme that synthesizes UDP-GlcNAc-an important component of the cell wall of many microorganisms. Uridyltransfer, one of the reactions it catalyzes, involves binding GlcNAc-1-P, UTP and Mg(2+) ions; however, whether one or two ions catalyze this reaction remains ambiguous. Here, we resolve this using biochemical and crystallographic studies on GlmU from Mycobacterium tuberculosis (GlmU(Mtb)) and identify a two-metal-ion mechanism (mechanism-B). In contrast to well-established two-metal mechanism (mechanism-A) for enzymes acting on nucleic acids, mechanism-B is distinct in the way the two Mg(2+) ions (Mg(2+)A and Mg(2+)B) are positioned and stabilized. Further, attempts to delineate the roles of the metal ions in substrate stabilization, nucleophile activation and transition-state stabilization are presented. Interestingly, a detailed analysis of the available structures of sugar nucleotidyl transferases (SNTs) suggests that they too would utilize mechanism-B rather than mechanism-A. Based on this, SNTs could be classified into Group-I, which employs the two-metal mechanism-B as in GlmU, and Group-II that employs a variant one-metal mechanism-B, wherein the role of Mg(2+)A is substituted by a conserved lysine. Strikingly, eukaryotic SNTs appear confined to Group-II. Recognizing these differences may be important in the design of selective inhibitors against microbial nucleotidyl transferases.


  • Organizational Affiliation

    Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional protein GlmU501Mycobacterium tuberculosisMutation(s): 0 
Gene Names: glmURv1018c
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMN3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.27α = 90
b = 79.27β = 90
c = 276.73γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary