The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 

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Nucleoside Binding Site of Herpes Simplex Type 1 Thymidine Kinase Analyzed by X-Ray Crystallography

Vogt, J.Perozzo, R.Pautsch, A.Prota, A.Schelling, P.Pilger, B.Folkers, G.Scapozza, L.Schulz, G.E.

(2000) Proteins 41: 545

  • DOI: https://doi.org/10.1002/1097-0134(20001201)41:4<545::aid-prot110>3.0.co;2-8
  • Primary Citation of Related Structures:  
    1E2H, 1E2I, 1E2J

  • PubMed Abstract: 

    The crystal structures of the full-length Herpes simplex virus type 1 thymidine kinase in its unligated form and in a complex with an adenine analogue have been determined at 1.9 A resolution. The unligated enzyme contains four water molecules in the thymidine pocket and reveals a small induced fit on substrate binding. The structure of the ligated enzyme shows for the first time a bound adenine analogue after numerous complexes with thymine and guanine analogues have been reported. The adenine analogue constitutes a new lead compound for enzyme-prodrug gene therapy. In addition, the structure of mutant Q125N modifying the binding site of the natural substrate thymidine in complex with this substrate has been established at 2.5 A resolution. It reveals that neither the binding mode of thymidine nor the polypeptide backbone conformation is altered, except that the two major hydrogen bonds to thymidine are replaced by a single water-mediated hydrogen bond, which improves the relative acceptance of the prodrugs aciclovir and ganciclovir compared with the natural substrate. Accordingly, the mutant structure represents a first step toward improving the virus-directed enzyme-prodrug gene therapy by enzyme engineering.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
331Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Find proteins for P0DTH5 (Human herpesvirus 1 (strain 17))
Explore P0DTH5 
Go to UniProtKB:  P0DTH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTH5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113α = 90
b = 116.9β = 90
c = 108γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description