1KI2

CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH GANCICLOVIR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.

Champness, J.N.Bennett, M.S.Wien, F.Visse, R.Summers, W.C.Herdewijn, P.de Clerq, E.Ostrowski, T.Jarvest, R.L.Sanderson, M.R.

(1998) Proteins 32: 350-361

  • Primary Citation of Related Structures:  1KI3, 1KI4, 1KI6, 1KI7, 1KI8, 1KIM

  • PubMed Abstract: 
  • Antiherpes therapies are principally targeted at viral thymidine kinases and utilize nucleoside analogs, the triphosphates of which are inhibitors of viral DNA polymerase or result in toxic effects when incorporated into DNA. The most frequently used ...

    Antiherpes therapies are principally targeted at viral thymidine kinases and utilize nucleoside analogs, the triphosphates of which are inhibitors of viral DNA polymerase or result in toxic effects when incorporated into DNA. The most frequently used drug, aciclovir (Zovirax), is a relatively poor substrate for thymidine kinase and high-resolution structural information on drugs and other molecules binding to the target is therefore important for the design of novel and more potent chemotherapy, both in antiherpes treatment and in gene therapy systems where thymidine kinase is expressed. Here, we report for the first time the binary complexes of HSV-1 thymidine kinase (TK) with the drug molecules aciclovir and penciclovir, determined by X-ray crystallography at 2.37 A resolution. Moreover, from new data at 2.14 A resolution, the refined structure of the complex of TK with its substrate deoxythymidine (R = 0.209 for 96% of all data) now reveals much detail concerning substrate and solvent interactions with the enzyme. Structures of the complexes of TK with four halogen-containing substrate analogs have also been solved, to resolutions better than 2.4 A. The various TK inhibitors broadly fall into three groups which together probe the space of the enzyme active site in a manner that no one molecule does alone, so giving a composite picture of active site interactions that can be exploited in the design of novel compounds.


    Related Citations: 
    • Nucleotide Sequence of the Thymidine Kinase Gene of Herpes Simplex Virus Type 1
      Wagner, M.J.,Sharp, J.A.,Summers, W.C.
      (1981) Proc.Natl.Acad.Sci.USA 78: 1441
    • 3'-Amino Thymidine Affinity Matrix for the Purification of Herpes Simplex Virus Thymidine Kinase
      Tung, P.P.,Respass, J.,Summers, W.C.
      (1996) Yale J.Biol.Med. 69: 495
    • The Complete DNA Sequence of the Long Unique Region in the Genome of Herpes Simplex Virus Type 1
      Mcgeoch, D.J.,Dalrymple, M.A.,Davison, A.J.,Dolan, A.,Frame, M.C.,Mcnab, D.,Perry, L.J.,Scott, J.E.,Taylor, P.
      (1988) J.Gen.Virol. 69: 1531
    • Purification and Crystallization of Thymidine Kinase from Herpes Simplex Virus Type 1
      Sanderson, M.R.,Freemont, P.S.,Murthy, H.M.,Krane, J.F.,Summers, W.C.,Steitz, T.A.
      (1988) J.Mol.Biol. 202: 917
    • Crystal Structures of the Thymidine Kinase from Herpes Simplex Virus Type-1 in Complex with Deoxythymidine and Ganciclovir
      Brown, D.G.,Visse, R.,Sandhu, G.,Davies, A.,Rizkallah, P.J.,Melitz, C.,Summers, W.C.,Sanderson, M.R.
      (1995) Nat.Struct.Mol.Biol. 2: 876


    Organizational Affiliation

    Division of Biomedical Sciences, Randall Institute, King's College, London, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDINE KINASE
A, B
331Human 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
GA2
Query on GA2

Download SDF File 
Download CCD File 
A, B
9-(1,3-DIHYDROXY-PROPOXYMETHANE)GUANINE
C9 H13 N5 O4
IRSCQMHQWWYFCW-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 114.900α = 90.00
b = 118.700β = 90.00
c = 109.100γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata scaling
R-AXISdata reduction
SOLOMONphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance