Glutaminase domain of glucosamine 6-phosphate synthase complexed with glutamate

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

Starting Model: experimental
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Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 Angstrom Crystal Structure of the Glutaminase Domain of Glucosamine 6-Phosphate Synthase

Isupov, M.N.Obmolova, G.Butterworth, S.Badet-Denisot, M.-A.Badet, B.Polikarpov, I.Littlechild, J.A.Teplyakov, A.

(1996) Structure 4: 801-810

  • DOI: https://doi.org/10.1016/s0969-2126(96)00087-1
  • Primary Citation of Related Structures:  
    1XFF, 1XFG

  • PubMed Abstract: 

    Amidotransferases use the amide nitrogen of glutamine in a number of important biosynthetic reactions. They are composed of a glutaminase domain, which catalyzes the hydrolysis of glutamine to glutamate and ammonia, and a synthetase domain, catalyzing amination of the substrate. To gain insight into the mechanism of nitrogen transfer, we examined the structure of the glutaminase domain of glucosamine 6-phosphate synthase (GLMS). The crystal structures of the enzyme complexed with glutamate and with a competitive inhibitor, Glu-hydroxamate, have been determined to 1.8 A resolution. The protein fold has structural homology to other members of the superfamily of N-terminal nucleophile (Ntn) hydrolases, being a sandwich of antiparallel beta sheets surrounded by two layers of alpha helices. The structural homology between the glutaminase domain of GLMS and that of PRPP amidotransferase (the only other Ntn amidotransferase whose structure is known) indicates that they may have diverged from a common ancestor. Cys1 is the catalytic nucleophile in GLMS, and the nucleophilic character of its thiol group appears to be increased through general base activation by its own alpha-amino group. Cys1 can adopt two conformations, one active and one inactive; glutamine binding locks the residue in a predetermined conformation. We propose that when a nitrogen acceptor is present Cys1 is kept in the active conformation, explaining the phenomenon of substrate-induced activation of the enzyme, and that Arg26 is central in this coupling.

  • Organizational Affiliation

    Department of Chemistry and Biological Sciences, University of Exeter, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
A, B
240Escherichia coliMutation(s): 0 
Gene Names: GLMS
Find proteins for P17169 (Escherichia coli (strain K12))
Explore P17169 
Go to UniProtKB:  P17169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17169
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.38α = 90
b = 82.52β = 90
c = 86.05γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description