PDBsum entry 1e2j

Transferase

PDB id: 1e2j

Contents

Protein chains

306 a.a. *

Ligands

SO4 ×2

THM ×2

Waters ×111

* Residue conservation analysis

PDB id:

1e2j

Name:

Transferase

Title:

The nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by x-ray crystallography

Structure:

Thymidine kinase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Herpes simplex virus (type 1/strain 17). Organism_taxid: 10299. Strain: 17. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.212 R-free: 0.273

Authors:

J.Vogt,L.Scapozza,G.E.Schulz

Key ref:

J.Vogt et al. (2000). Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography. Proteins, 41, 545-553. PubMed id: 11056041 DOI: 10.1002/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8

Date:

23-May-00 Release date: 06-Nov-00

Protein chains

P0DTH5  (KITH_HHV11) -  Thymidine kinase from Human herpesvirus 1 (strain 17)

Seq: 376 a.a.

Struc: 306 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.1.21 - thymidine kinase.
• Reaction: thymidine + ATP = dTMP + ADP + H⁺

thymidine + ATP (Bound ligand (Het Group name = THM) corresponds exactly) = dTMP + ADP + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8

Proteins 41:545-553 (2000)

PubMed id: 11056041

Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography.

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

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.

Selected figure(s)

Figure 3.
Figure 3. Structural formulae of the adenosine analogue 9-(2-(S)-hydroxypropyl)adenine (HPA) and the AMP analogue 9-(2-phosphonylmethoxyethyl)adenine (PMEA). HPA was used as a racemic mixture.

Figure 6.
Figure 6. Superposition of mutant TK[HSV1](Q125N) in complex with dT (thick solid lines, C atoms marked by small dots, hydrogen bonds are dotted) with wild-type TK[HSV1] in complex with aciclovir (thin solid lines),[19] ganciclovir (thin dotted lines)[19]and dT (thick dotted lines).[19] For sake of clarity, side chains are only drawn for TK[HSV1](Q125N):dT and TK[HSV1]:aciclovir. Water molecules and hydrogen bonds are depicted for TK[HSV1](Q125N):dT (black circles) and TK[HSV1]:aciclovir (pale circles). For aciclovir, only the location of the hydroxyl group at the 5 -OH position of dT is shown.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 41, 545-553) copyright 2000.

Figures were selected by the author.