1E98

Wild type human thymidylate kinase complexed with AZTMP and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1006/jmbi.2000.4175
  • Primary Citation of Related Structures:  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 ...

    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.


    Related Citations: 
    • Insights Into the Phosphoryl Transfer Mechanism of Human Thymidylate Kinase Gained by 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE KINASE
A
215Homo sapiensGene Names: DTYMK (CDC8, TMPK, TYMK)
EC: 2.7.4.9
Find proteins for P23919 (Homo sapiens)
Go to Gene View: DTYMK
Go to UniProtKB:  P23919
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATM
Query on ATM

Download SDF File 
Download CCD File 
A
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
OIFWQOKDSPDILA-XLPZGREQSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.050α = 90.00
b = 101.050β = 90.00
c = 49.950γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-05
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance