1E2J

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

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

  • 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 ...

    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.

    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
    • 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 Biol 2: 876
    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 KINASEA, B331Human alphaherpesvirus 1 strain 17Mutation(s): 1 
Gene Names: TK, UL23
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
THM
Query on THM
Download Ideal Coordinates CCD File 
A, B
THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
THMIC50:  1000   nM  BindingDB
THMΔH:  73.08000183105469   kJ/mol  BindingDB
THMΔH:  57.119998931884766   kJ/mol  BindingDB
THMΔH:  66.36000061035156   kJ/mol  BindingDB
THMΔG:  29.399999618530273   kJ/mol  BindingDB
THM-TΔS:  50.09000015258789   kJ/mol  BindingDB
THM-TΔS:  27.18000030517578   kJ/mol  BindingDB
THMΔG:  29.81999969482422   kJ/mol  BindingDB
THM-TΔS:  42.79999923706055   kJ/mol  BindingDB
THMΔH:  79.91000366210938   kJ/mol  BindingDB
THMΔG:  30.239999771118164   kJ/mol  BindingDB
THM-TΔS:  36.880001068115234   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.4α = 90
b = 117.5β = 90
c = 108.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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: 2017-07-05
    Changes: Data collection