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Catalytic Site Atlas

CSA LITERATURE entry for 1kim

E.C. namethymidine kinase
SpeciesHuman herpesvirus 1 (Virus)
E.C. Number (IntEnz)
CSA Homologues of 1kimThere are 47 Homologs
CSA Entries With UniProtID P03176
CSA Entries With EC Number
PDBe Entry 1kim
PDBSum Entry 1kim
MACiE Entry 1kim

Literature Report

IntroductionThymidine kinases (TK) are key enzymes in the pyrimidine salvage pathway catalyzing the phosphate transfer from ATP to thymidine (dT) in the presence of Mg2+ and thus, yielding thymidine monophosphate (dTMP) and ADP. Herpesviridae, such as Herpes simplex virus type 1, encode for their own, multifunctional TK. Unlike the very specific human cytosolic TK (TK1), it is able to phosphorylate pyrimidine as well as purine analogs and demands less stereochemical restrictions concerning the sugar moiety also accepting acyclic side chains as phosphate acceptors (e.g., aciclovir). Therefore, the difference in substrate specificity of human TK 1 and TKHSV1 is a crucial point in establishing a molecular basis for selective antiviral therapy, featuring TKHSV1 as the center of activation of antiviral drugs such as aciclovir (ACV), penciclovir, and ganciclovir (GCV). First being activated by phosphorylation by viral encoded TK, these nucleoside analogs in their triphosphate form block the viral replication by subsequently terminating DNA elongation at the viral DNA polymerase. In combination with GCV TKHSV1 is an established tool used as a prodrug-activating enzyme, so-called suicide enzyme, in gene therapy of cancer, AIDS, and in controlling graft-versus-host disease by allogenic bone marrow transplant (allo BMT).
MechansimThe catalytic mechanism proceeds as follows: (1) Glu83 acts as a general base to activate the acceptor group, 5'-hydroxyl group of thymidine. (2) The activated acceptor group makes a nucleophilic attack on the transferred group, gamma-phosphate of ATP. (3) During the transition state, the transferred group and leaving group (beta- and alpha-phosphate groups of ATP) must be stabilized by stabilizer residues, Arg/Lys cluster, along with the magnesium ion as cofactor.
Note: Although there has been no structure with magnesium ion bound to the active site, this enzyme should bind a magnesium ion as cofactor to the side chains of Thr63 and Asp162.

Catalytic Sites for 1kim

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA8383macie:sideChainActs as a general base to deprotonate the O-5' atom to increase its nucleophilicity and activate it for attack.
ArgA222222macie:sideChainForms an anion hole to make the phosphate atom more electrophilic.
ArgA220220macie:sideChainForms an anion hole to make the phosphate atom more electrophilic.
ArgA163163macie:sideChainStabilise transition group to aid transfer. Also could position the thymidine for phosphorylation.
LysA6262macie:sideChainLys62 was suggested to aid the gamma-phosphoryl transfer during catalysis via stabilisation of the transition state.
GluA225225macie:sideChainImportant dipole interaction with sugar moiety

Literature References

Sulpizi M
The rational of catalytic activity of herpes simplex virus thymidine kinase. a combined biochemical and quantum chemical study.
J Biol Chem 2001 276 21692-21697
PubMed: 11262392
Champness JN
Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.
Proteins 1998 32 350-361
PubMed: 9715911
Wild K
The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.
Protein Sci 1997 6 2097-2106
PubMed: 9336833