1E9F

Mutant human thymidylate kinase complexed with TMP and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Potentiating Azt Activation: Structures of Wildtype and Mutant Human Thymidylate Kinase Suggest Reasons for the Mutants' Improved Kinetics with the HIV Prodrug Metabolite Aztmp

Ostermann, N.Lavie, A.Padiyar, S.Brundiers, R.Veit, T.Reintein, J.Goody, R.S.Konrad, M.Schlichting, I.

(2000) J Mol Biol 304: 43

  • DOI: https://doi.org/10.1006/jmbi.2000.4175
  • Primary Citation of Related Structures:  
    1E98, 1E99, 1E9A, 1E9B, 1E9C, 1E9D, 1E9E, 1E9F

  • PubMed Abstract: 

    The 60-fold reduced phosphorylation rate of azidothymidine (AZT) monophosphate (AZTMP), the partially activated AZT metabolite, by human thymidylate kinase (TMPK) severely limits the efficacy of this anti-HIV prodrug. Crystal structures of different TMPK nucleotide complexes indicate that steric hindrance by the azido group of AZTMP prevents formation of the catalytically active closed conformation of the P-loop of TMPK. The F105Y mutant and a chimeric mutant that contains sequences of the human and Escherichia coli enzyme phosphorylate AZTMP 20-fold faster than the wild-type enzyme. The structural basis of the increased activity is assigned to stabilization of the closed P-loop conformation.


  • Organizational Affiliation

    Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11 D-44227 Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THYMIDYLATE KINASE217Homo sapiensEscherichia coliMutation(s): 2 
EC: 2.7.4.9
UniProt & NIH Common Fund Data Resources
Find proteins for P0A720 (Escherichia coli (strain K12))
Explore P0A720 
Go to UniProtKB:  P0A720
Find proteins for P23919 (Homo sapiens)
Explore P23919 
Go to UniProtKB:  P23919
PHAROS:  P23919
GTEx:  ENSG00000168393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0A720P23919
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.2α = 90
b = 100.2β = 90
c = 49.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-11
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2019-07-24
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other