2WVJ

Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Comparative Active-Site Mutation Study of Human and Caenorhabditis Elegans Thymidine Kinase 1.

Skovgaard, T., Uhlin, U., Munch-Petersen, B.

(2012) FEBS J. 279: 1777

  • DOI: 10.1111/j.1742-4658.2012.08554.x

  • PubMed Abstract: 

    • The first step for the intracellular retention of several anticancer or antiviral nucleoside analogues is the addition of a phosphate group catalysed by a deoxyribonucleoside kinase such as thymidine kinase 1 (TK1). Recently, human TK1 (HuTK1) has be ...

    The first step for the intracellular retention of several anticancer or antiviral nucleoside analogues is the addition of a phosphate group catalysed by a deoxyribonucleoside kinase such as thymidine kinase 1 (TK1). Recently, human TK1 (HuTK1) has been crystallized and characterized using different ligands. To improve our understanding of TK1 substrate specificity, we performed a detailed, mutation-based comparative structure-function study of the active sites of two thymidine kinases: HuTK1 and Caenorhabditis elegans TK1 (CeTK1). Specifically, mutations were introduced into the hydrophobic pocket surrounding the substrate base. In CeTK1, some of these mutations led to increased activity with deoxycytidine and deoxyguanosine, two unusual substrates for TK1-like kinases. In HuTK1, mutation of T163 to S resulted in a kinase with a 140-fold lower K(m) for the antiviral nucleoside analogue 3'-azido-3'-deoxythymidine (AZT) compared with the natural substrate thymidine. The crystal structure of the T163S-mutated HuTK1 reveals a less ordered conformation of the ligand thymidine triphosphate compared with the wild-type structure but the cause of the changed specificity towards AZT is not obvious. Based on its highly increased AZT activity relative to thymidine activity this TK1 mutant could be suitable for suicide gene therapy.

    Organizational Affiliation: 

    Department of Science, Systems and Models, Roskilde University, Denmark. tine.skovgaard@cpr.ku.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDINE KINASE, CYTOSOLIC
A, B, C, D, E, F, G, H
193Homo sapiensMutation(s): 1 
Gene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
TTP
Query on TTP
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
D, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.902α = 90.00
b = 123.252β = 132.98
c = 121.024γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Database references, Derived calculations, Version format compliance