Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate and a magnesium-ion

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 

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This is version 1.5 of the entry. See complete history


Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained from Crystal Structures of Enzyme Complexes Along the Reaction Coordinate

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

(2000) Structure 8: 629

  • DOI: https://doi.org/10.1016/s0969-2126(00)00149-0
  • Primary Citation of Related Structures:  
    1E2D, 1E2E, 1E2F, 1E2G, 1E2Q

  • PubMed Abstract: 

    Thymidylate kinase (TMPK) is a nucleoside monophosphate kinase that catalyzes the reversible phosphoryltransfer between ATP and TMP to yield ADP and TDP. In addition to its vital role in supplying precursors for DNA synthesis, human TMPK has an important medical role participating in the activation of a number of anti-HIV prodrugs. Crystal structures of human TMPK in complex with TMP and ADP, TMP and the ATP analog AppNHp, TMP with ADP and the phosphoryl analog AlF(3), TDP and ADP, and the bisubstrate analog TP(5)A were determined. The conformations of the P-loop, the LID region, and the adenine-binding loop vary according to the nature of the complex. Substitution of ADP by AppNHp results in partial closure of the P-loop and the rotation of the TMP phosphate group to a catalytically unfavorable position, which rotates back in the AlF(3) complex to a position suitable for in-line attack. In the fully closed state observed in the TP(5)A and the TDP-ADP complexes, Asp15 interacts strongly with the 3'-hydroxyl group of TMP. The observed changes of nucleotide state and conformation and the corresponding protein structural changes are correlated with intermediates occurring along the reaction coordinate and show the sequence of events occurring during phosphate transfer. The low catalytic activity of human TMPK appears to be determined by structural changes required to achieve catalytic competence and it is suggested that a mechanism might exist to accelerate the activity.

  • Organizational Affiliation

    Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Dortmund, 44227, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THYMIDYLATE KINASE215Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
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 GroupP23919
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.3α = 90
b = 101.3β = 90
c = 49.3γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata 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: 2001-05-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other