Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution.

Horjales, E.Altamirano, M.M.Calcagno, M.L.Garratt, R.C.Oliva, G.

(1999) Structure 7: 527-537

  • DOI: https://doi.org/10.1016/s0969-2126(99)80069-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The allosteric hexameric enzyme glucosamine-6-phosphate deaminase from Escherichia coli catalyses the regulatory step of N-acetylglucosamine catabolism, which consists of the isomerisation and deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonia. The reversibility of the catalysis and its rapid-equilibrium random kinetic mechanism, among other properties, make this enzyme a good model for studying allosteric processes. Here we present the structure of P6(3)22 crystals, obtained in sodium acetate, of GlcN6P deaminase in its ligand-free T state. These crystals are very sensitive to X-ray radiation and have a high (78%) solvent content. The activesite lid (residues 162-185) is highly disordered in the T conformer; this may contribute significantly to the free-energy change of the whole allosteric transition. Comparison of the structure with the crystallographic coordinates of the R conformer (Brookhaven Protein Data Bank entry 1 dea) allows us to describe the geometrical changes associated with the allosteric transition as the movement of two rigid entities within each monomer. The active site, located in a deep cleft between these two rigid entities, presents a more open geometry in the T conformer than in the R conformer. The differences in active-site geometry are related to alterations in the substrate-binding properties associated with the allosteric transition. The rigid nature of the two mobile structural units of each monomer seems to be essential in order to explain the observed kinetics of the deaminase hexamer. The triggers for both the homotropic and heterotropic allosteric transitions are discussed and particular residues are assigned to these functions. A structural basis for an entropic term in the allosteric transition is an interesting new feature that emerges from this study.

  • Organizational Affiliation

    Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mor, Mexico. horjales@ibt.unam.mx

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (GLUCOSAMINE 6-PHOSPHATE DEAMINASE)266Escherichia coli K-12Mutation(s): 0 
Find proteins for P0A759 (Escherichia coli (strain K12))
Explore P0A759 
Go to UniProtKB:  P0A759
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A759
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.81α = 90
b = 129.81β = 90
c = 139.11γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
CCP4data scaling
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Refinement description