Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GDP

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase

Hible, G.Renault, L.Schaeffer, F.Christova, P.Radulescu, A.Z.Evrin, C.Gilles, A.M.Cherfils, J.

(2005) J Mol Biol 352: 1044-1059

  • DOI: https://doi.org/10.1016/j.jmb.2005.07.042
  • Primary Citation of Related Structures:  
    2AN9, 2ANB, 2ANC

  • PubMed Abstract: 

    Guanosine monophosphate kinases (GMPKs), which catalyze the phosphorylation of GMP and dGMP to their diphosphate form, have been characterized as monomeric enzymes in eukaryotes and prokaryotes. Here, we report that GMPK from Escherichia coli (ecGMPK) assembles in solution and in the crystal as several different oligomers. Thermodynamic analysis of ecGMPK using differential scanning calorimetry shows that the enzyme is in equilibrium between a dimer and higher order oligomers, whose relative amounts depend on protein concentration, ionic strength, and the presence of ATP. Crystallographic structures of ecGMPK in the apo, GMP and GDP-bound forms were solved at 3.2A, 2.9A and 2.4A resolution, respectively. ecGMPK forms a hexamer with D3 symmetry in all crystal forms, in which the two nucleotide-binding domains are able to undergo closure comparable to that of monomeric GMPKs. The 2-fold and 3-fold interfaces involve a 20-residue C-terminal extension and a sequence signature, respectively, that are missing from monomeric eukaryotic GMPKs, explaining why ecGMPK forms oligomers. These signatures are found in GMPKs from proteobacteria, some of which are human pathogens. GMPKs from these bacteria are thus likely to form the same quaternary structures. The shift of the thermodynamic equilibrium towards the dimer at low ecGMPK concentration together with the observation that inter-subunit interactions partially occlude the ATP-binding site in the hexameric structure suggest that the dimer may be the active species at physiological enzyme concentration.

  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette 91198, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanylate kinase
A, B
207Escherichia coliMutation(s): 0 
Gene Names: gmk
Find proteins for P60546 (Escherichia coli (strain K12))
Explore P60546 
Go to UniProtKB:  P60546
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60546
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.225α = 90
b = 68.225β = 90
c = 151.272γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description