2ORV

human Thymidine Kinase 1 in complex with TP4A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of ATP to TK1-like Enzymes Is Associated with a Conformational Change in the Quaternary Structure.

Segura-Pena, D.Lutz, S.Monnerjahn, C.Konrad, M.Lavie, A.

(2007) J.Mol.Biol. 369: 129-141

  • DOI: 10.1016/j.jmb.2007.02.104
  • Primary Citation of Related Structures:  2ORW

  • PubMed Abstract: 
  • Human thymidine kinase 1 (hTK1) and structurally related TKs from other organisms catalyze the initial phosphorylation step in the thymidine salvage pathway. Though ATP is known to be the preferred phosphoryl donor for TK1-like enzymes, its exact bin ...

    Human thymidine kinase 1 (hTK1) and structurally related TKs from other organisms catalyze the initial phosphorylation step in the thymidine salvage pathway. Though ATP is known to be the preferred phosphoryl donor for TK1-like enzymes, its exact binding mode and effect on the oligomeric state has not been analyzed. Here we report the structures of hTK1 and of the Thermotoga maritima thymidine kinase (TmTK) in complex with the bisubstrate inhibitor TP4A. The TmTK-TP4A structure reveals that the adenosine moiety of ATP binds at the subunit interface of the homotetrameric enzyme and that the majority of the ATP-enzyme interactions occur between the phosphate groups and the P-loop. In the hTK1 structure the adenosine group of TP4A exhibited no electron density. This difference between hTK1 and TmTK is rationalized by a difference in the conformation of their quaternary structure. A more open conformation, as seen in the TmTK-TP4A complex structure, is required to provide space for the adenosine moiety. Our analysis supports the formation of an analogous open conformation in hTK1 upon ATP binding.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, IL 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidine kinase
A, B
234Homo sapiensGene Names: TK1
EC: 2.7.1.21
Find proteins for P04183 (Homo sapiens)
Go to Gene View: TK1
Go to UniProtKB:  P04183
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
4TA
Query on 4TA

Download SDF File 
Download CCD File 
A, B
P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
C20 H25 N7 O20 P4
WLGHSSFVEUABFP-SLFMBYJQSA-J
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4TAKd: 29 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.980α = 90.00
b = 80.980β = 90.00
c = 156.360γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata scaling
REFMACrefinement
SOLVEphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance