PDBsum entry 1of1

Transferase

PDB id: 1of1

Contents

Protein chains

308 a.a. *

Ligands

SCT ×2

SO4 ×2

Waters ×340

* Residue conservation analysis

PDB id:

1of1

Name:

Transferase

Title:

Kinetics and crystal structure of the herpes simplex virus type 1 thymidine kinase interacting with (south)-methanocarba-thymidine

Structure:

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

Source:

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

Biol. unit:

Dimer (from PDB file)

Resolution:

1.95Å R-factor: 0.184 R-free: 0.218

Authors:

M.T.Claus,P.Schelling,G.Folkers,V.E.Marquez,L.Scapozza,G.E.Schulz

Key ref:

P.Schelling et al. (2004). Biochemical and structural characterization of (South)-methanocarbathymidine that specifically inhibits growth of herpes simplex virus type 1 thymidine kinase-transduced osteosarcoma cells. J Biol Chem, 279, 32832-32838. PubMed id: 15163659 DOI: 10.1074/jbc.M313343200

Date:

03-Apr-03 Release date: 03-Jun-04

Protein chains

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

Seq: 376 a.a.

Struc: 308 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 = SCT) matches with 84.21% similarity) = dTMP + ADP + H(+)

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

reference

DOI no: 10.1074/jbc.M313343200

J Biol Chem 279:32832-32838 (2004)

PubMed id: 15163659

Biochemical and structural characterization of (South)-methanocarbathymidine that specifically inhibits growth of herpes simplex virus type 1 thymidine kinase-transduced osteosarcoma cells.

P.Schelling, M.T.Claus, R.Johner, V.E.Marquez, G.E.Schulz, L.Scapozza.

ABSTRACT

Two analogs of the natural nucleoside dT featuring a pseudosugar with fixed conformation in place of the deoxyribosyl residue (carbathymidine analogs) were biochemically and structurally characterized for their acceptance by both human cytosolic thymidine kinase isoenzyme 1 (hTK1) and herpes simplex virus type 1 thymidine kinase (HSV1 TK) and subsequently tested in cell proliferation assays. 3'-exo-Methanocarbathymidine ((South)-methanocarbathymidine (S)-MCT), which is a substrate for HSV1 TK, specifically inhibited growth of HSV1 TK-transduced human osteosarcoma cells with an IC(50) value in the range of 15 microM without significant toxicity toward both hTK1-negative (TK(-)) and non-transduced cells. 2'-exo-Methanocarbathymidine ((North)-methanocarbathymidine (N)-MCT), which is a weak substrate for hTK1 and a substantial one for HSV1 TK, induced a specific growth inhibition in HSV1 TK-transfected cells comparable to that of (S)-MCT and ganciclovir. A growth inhibition activity was also observed with (N)-MCT and ganciclovir in non-transduced cells in a cell line-dependent manner, whereas TK(-) cells were not affected. The presented 1.95-A crystal structure of the complex (S)-MCT.HSV1 TK explains both the more favorable binding affinity and catalytic turnover of (S)-MCT for HSV1 TK over the North analog. Additionally the plasticity of the active site of the enzyme is addressed by comparing the binding of (North)- and (South)-carbathymidine analogs. The presented study of these two potent candidate prodrugs for HSV1 TK gene-directed enzyme prodrug therapy suggests that (S)-MCT may be even safer to use than its North counterpart (N)-MCT.

Selected figure(s)

Figure 1.
FIG. 1. Structures of (N)-MCT (A) and (S)-MCT (B).

Figure 5.
FIG. 5. Stereoview of HSV1 TK structure in complex with (S)-MCT. The conformation of the compound and the position of the sulfate group are well defined by the electron density contoured at 1.3 . The hydrogen bonding patterns for the thymine moiety as well as for both 3'-OH and 5'-OH groups are the same as in the HSV1 TK·dT structure. (S)-MCT and HSV1 TK carbon atoms are represented in orange and black; nitrogen, oxygen, and sulfur atoms are in blue, red, and yellow, respectively; and water molecules are represented as green balls. H-bonds are depicted by dashed lines between donor (D) and acceptor (A) and defined as follows: distance D--A, 2.8-3.2 Å; angle D-H--A, 140-180°.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 32832-32838) copyright 2004.

Figures were selected by an automated process.