Abstract
Despite its importance in the nucleoside (and nucleoside prodrug) metabolism, the structure of the active conformation of human thymidine kinase 1 (hTK1) remains elusive. We perform microsecond molecular dynamics simulations of the inactive enzyme form bound to a bisubstrate inhibitor that was shown experimentally to activate another TK1-like kinase, Thermotoga maritima TK (TmTK). Our results are in excellent agreement with the experimental findings for the TmTK closed-to-open state transition. We show that the inhibitor induces an increase of the enzyme radius of gyration due to the expansion on one of the dimer interfaces; the structural changes observed, including the active site pocket volume increase and the decrease in the monomer–monomer buried surface area and of the number of hydrogen bonds (as compared to the inactive enzyme control simulation), indicate that the catalytically competent (open) conformation of hTK1 can be assumed in the presence of an activating ligand.
Highlights
IntroductionHuman thymidine kinase 1 (hTK1) is a phosphotransferase that catalyzes phosphoryl transfer from adenine triphosphate (ATP) to thymidine (T) using glutamic acid, Glu[98], as a proton acceptor (Figure 1).[1] The enzyme, crucial for nucleoside metabolism related to DNA synthesis, is clinically important for the activation of otherwise nontoxic prodrugs such as azidothymidine, cytarabine, acyclovir,[1,2] and potentially radiosensitizing nucleosides that have to be incorporated into DNA prior to its radiation-induced damage
Human thymidine kinase 1 is a phosphotransferase that catalyzes phosphoryl transfer from adenine triphosphate (ATP) to thymidine (T) using glutamic acid, Glu[98], as a proton acceptor (Figure 1).[1]
The overall volume of the enzyme is increasing upon binding the bisubstrate inhibitor, as the enzyme expands on the weak dimer interface
Summary
Human thymidine kinase 1 (hTK1) is a phosphotransferase that catalyzes phosphoryl transfer from adenine triphosphate (ATP) to thymidine (T) using glutamic acid, Glu[98], as a proton acceptor (Figure 1).[1] The enzyme, crucial for nucleoside metabolism related to DNA synthesis, is clinically important for the activation of otherwise nontoxic prodrugs such as azidothymidine, cytarabine, acyclovir,[1,2] and potentially radiosensitizing nucleosides that have to be incorporated into DNA prior to its radiation-induced damage. HTK1 is readily inhibited (and the enzyme conformation assumes its closed form) by the feedback inhibitor, thymidine triphosphate (TTP), which binds to the phosphoryl acceptor-binding site.[12]
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