2VTK

THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.

Wild, K.Bohner, T.Folkers, G.Schulz, G.E.

(1997) Protein Sci 6: 2097-2106

  • DOI: 10.1002/pro.5560061005
  • Primary Citation of Related Structures:  
    3VTK, 2VTK, 1VTK

  • PubMed Abstract: 
  • Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N-terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP), deoxythymidine (dT), or id ...

    Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N-terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP), deoxythymidine (dT), or idoxuridine-5'-phosphate (5-iodo-dUMP) at the substrate-site were refined to 2.75 A, 2.8 A, and 3.0 A resolution, respectively. TK catalyzes the phosphorylation of dT resulting in an ester, and the phosphorylation of dTMP giving rise to an anhydride. The presented TK structures indicate that there are only small differences between these two modes of action. Glu83 serves as a general base in the ester reaction. Arg163 parks at an internal aspartate during ester formation and binds the alpha-phosphate of dTMP during anhydride formation. The bound deoxythymidine leaves a 35 A3 cavity at position 5 of the base and two sequestered water molecules at position 2. Cavity and water molecules reduce the substrate specificity to such an extent that TK can phosphorylate various substrate analogues useful in pharmaceutical applications. TK is structurally homologous to the well-known nucleoside monophosphate kinases but contains large additional peptide segments.


    Related Citations: 
    • The Three-Dimensional Structure of Thymidine Kinase from Herpes Simplex Virus Type 1
      Wild, K., Bohner, T., Aubry, A., Folkers, G., Schulz, G.E.
      (1995) FEBS Lett 368: 289
    • A Fast Method for Obtaining Highly Pure Recombinant Herpes Simplex Virus Type 1 Thymidine Kinase
      Fetzer, J., Michael, M., Bohner, T., Hofbauer, R., Folkers, G.
      (1994) Protein Expr Purif 5: 432

    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDINE KINASEA343Human alphaherpesvirus 1 strain FMutation(s): 0 
EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17))
Explore P03176 
Go to UniProtKB:  P03176
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download Ideal Coordinates CCD File 
A
THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
THMIC50:  1000   nM  BindingDB
THMΔH:  73.08000183105469   kJ/mol  BindingDB
THMΔH:  79.91000366210938   kJ/mol  BindingDB
THMΔH:  66.36000061035156   kJ/mol  BindingDB
THM-TΔS:  36.880001068115234   kJ/mol  BindingDB
THMΔG:  29.399999618530273   kJ/mol  BindingDB
THM-TΔS:  27.18000030517578   kJ/mol  BindingDB
THM-TΔS:  50.09000015258789   kJ/mol  BindingDB
THMΔG:  29.81999969482422   kJ/mol  BindingDB
THMΔH:  57.119998931884766   kJ/mol  BindingDB
THM-TΔS:  42.79999923706055   kJ/mol  BindingDB
THMΔG:  30.239999771118164   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.1α = 90
b = 84.1β = 90
c = 155.36γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
MERGEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1997-04-01 
  • Released Date: 1997-10-22 
  • Deposition Author(s): Wild, K., Schulz, G.E.

Revision History 

  • Version 1.0: 1997-10-22
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance