Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 174.96 kDa 
• Atom Count: 11307 
• Modelled Residue Count: 1290 
• Deposited Residue Count: 1544 
• Unique protein chains: 1

2WVJ

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

• PDB DOI: 10.2210/pdb2WVJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2009-10-17 Released: 2009-10-27 
• Deposition Author(s): Skovgaard, T., Uhlin, U., Munch-Petersen, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

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

• PubMed: 22385435 
• DOI: 10.1111/j.1742-4658.2012.08554.x
• Primary Citation of Related Structures:  
  2WVJ


• 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 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.

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Organizational Affiliation: 

Department of Science, Systems and Models, Roskilde University, Denmark. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDINE KINASE, CYTOSOLIC	A, B, C, D, E, F, G, H	193	Homo sapiens	Mutation(s): 1  Gene Names: TK1 EC: 2.7.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P04183 (Homo sapiens) Explore P04183  Go to UniProtKB:  P04183
PHAROS:  P04183 GTEx:  ENSG00000167900

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	I [auth A], K [auth B], M [auth C], O [auth D], R [auth E], T [auth F], V [auth G], Y [auth H]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
ZN	AA [auth H], J [auth A], L [auth B], N [auth C], Q [auth D], S [auth E], U [auth F], X [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	P [auth D], W [auth G], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.902	α = 90
b = 123.252	β = 132.98
c = 121.024	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-17 
• Released Date: 2009-10-27 
Deposition Author(s): Skovgaard, T., Uhlin, U., Munch-Petersen, B.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2012-05-02
  Changes: Database references, Derived calculations, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other