3VTK

THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND 5-IODO-DEOXYURIDINE-MONOPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.222 

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:  1VTK, 2VTK

  • 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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDINE KINASE
A
343Human herpesvirus 1 (strain 17)Gene Names: TK
EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17))
Go to UniProtKB:  P03176
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
A
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 I N2 O8 P
WXFYBFRZROJDLL-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.222 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 83.700α = 90.00
b = 83.700β = 90.00
c = 156.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MERGEdata scaling
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance