Crystal structure of mouse guanylate kinase in complex with GMP and ADP

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 

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Structural characterization of the closed conformation of mouse guanylate kinase.

Sekulic, N.Shuvalova, L.Spangenberg, O.Konrad, M.Lavie, A.

(2002) J Biol Chem 277: 30236-30243

  • DOI: https://doi.org/10.1074/jbc.M204668200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Guanylate kinase (GMPK) is a nucleoside monophosphate kinase that catalyzes the reversible phosphoryl transfer from ATP to GMP to yield ADP and GDP. In addition to phosphorylating GMP, antiviral prodrugs such as acyclovir, ganciclovir, and carbovir and anticancer prodrugs such as the thiopurines are dependent on GMPK for their activation. Hence, structural information on mammalian GMPK could play a role in the design of improved antiviral and antineoplastic agents. Here we present the structure of the mouse enzyme in an abortive complex with the nucleotides ADP and GMP, refined at 2.1 A resolution with a final crystallographic R factor of 0.19 (R(free) = 0.23). Guanylate kinase is a member of the nucleoside monophosphate (NMP) kinase family, a family of enzymes that despite having a low primary structure identity share a similar fold, which consists of three structurally distinct regions termed the CORE, LID, and NMP-binding regions. Previous studies on the yeast enzyme have shown that these parts move as rigid bodies upon substrate binding. It has been proposed that consecutive binding of substrates leads to "closing" of the active site bringing the NMP-binding and LID regions closer to each other and to the CORE region. Our structure, which is the first of any guanylate kinase with both substrates bound, supports this hypothesis. It also reveals the binding site of ATP and implicates arginines 44, 137, and 148 (in addition to the invariant P-loop lysine) as candidates for catalyzing the chemical step of the phosphoryl transfer.

  • Organizational Affiliation

    University of Illinois at Chicago, Department of Biochemistry and Molecular Biology, Chicago, Illinois 60612 and the Max Planck Institute for Biophysical Chemistry, Department of Molecular Genetics, Am Fassberg 11, 37077 Göttingen, Germany.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanylate kinase198Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q64520 (Mus musculus)
Explore Q64520 
Go to UniProtKB:  Q64520
IMPC:  MGI:95871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64520
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.241α = 90
b = 67.241β = 90
c = 108.696γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata 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: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description