1E2H

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

Summary for 1E2H

• Entry DOI: 10.2210/pdb1e2h/pdb
• Related: 1E2I 1E2J 1E2K 1E2L 1E2M 1E2N 1E2P 1KI2 1KI4 1KI5 1KI6 1KI7 1KI8 1KIM 1VTK 2VTK 3VTK
• Descriptor: THYMIDINE KINASE, SULFATE ION (3 entities in total)
• Functional Keywords: transferase, adenine analog, enzyme-prodrug gene therapy, nucleoside- binding, thymidine kinase
• Biological source: HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
• Total number of polymer chains: 2
• Total formula weight: 71750.30

Authors

Vogt, J.,Scapozza, L.,Schulz, G.E. (deposition date: 2000-05-23, release date: 2000-11-06, Last modification date: 2023-12-06)

Primary citation

Vogt, J.,Perozzo, R.,Pautsch, A.,Prota, A.,Schelling, P.,Pilger, B.,Folkers, G.,Scapozza, L.,Schulz, G.E.
Nucleoside Binding Site of Herpes Simplex Type 1 Thymidine Kinase Analyzed by X-Ray Crystallography
Proteins: Struct.,Funct., Genet., 41:545-, 2000

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.

PubMed: 11056041
DOI: 10.1002/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8

Experimental method

X-RAY DIFFRACTION (1.9 Å)