The crystal structures of Escherichia coli thymidylate kinase (TmpK) in complex with P 1 -(5-adenosyl)-P 5 -(5-thymidyl)pentaphosphate and P 1 -(5-adenosyl)P 5 -[5-(3-azido-3-deoxythymidine)] pentaphosphate have been solved to 2.0-Å and 2.2-Å resolution, respectively. The overall structure of the bacterial TmpK is very similar to that of yeast TmpK. In contrast to the human and yeast TmpKs, which phosphorylate 3-azido-3-deoxythymidine 5-monophosphate (AZT-MP) at a 200-fold reduced turnover number (k cat ) in comparison to the physiological substrate dTMP, reduction of k cat is only 2-fold for the bacterial enzyme. The different kinetic properties toward AZT-MP between the eukaryotic TmpKs and E. coli TmpK can be rationalized by the different ways in which these enzymes stabilize the presumed transition state and the different manner in which a carboxylic acid side chain in the P loop interacts with the deoxyribose of the monophosphate. Yeast TmpK interacts with the 3-hydroxyl of dTMP through Asp-14 of the P loop in a bidentate manner: binding of AZT-MP results in a shift of the P loop to accommodate the larger substituent. In E. coli TmpK, the corresponding residue is Glu-12, and it interacts in a side-on fashion with the 3-hydroxyl of dTMP. This different mode of interaction between the P loop carboxylic acid with the 3 substituent of the monophosphate deoxyribose allows the accommodation of an azido group in the case of the E. coli enzyme without significant P loop movement. In addition, although the yeast enzyme uses Arg-15 (a glycine in E. coli) to stabilize the transition state, E. coli seems to use Arg-153 from a region termed Lid instead. Thus, the binding of AZT-MP to the yeast TmpK results in the shift of a catalytic residue, which is not the case for the bacterial kinase.Phosphorylation of AZT-MP by thymidylate kinase (TmpK; EC 2.7.4.9, ATP:dTMP phosphotransferase) has been implicated as the rate-limiting step in the activation pathway of the anti-HIV prodrug 3Ј-azido-3Ј-deoxythymidine (AZT). AZT must be phosphorylated by cellular enzymes to azidothymidine triphosphate before it can exert its antiviral effect by inhibiting HIV reverse transcriptase and acting as a chain terminator of nascent DNA strands. The bottleneck of AZT activation lies in the second phosphorylation step, the step that adds a phosphate group to azidothymidine monophosphate (AZT-MP) to yield azidothymidine diphosphate and is catalyzed by TmpK. Cells treated with AZT accumulate the toxic AZT-MP (1-3) in millimolar concentration (4, 5), and thus the active AZT triphosphorylated metabolite is at very low concentration. This situation is only slightly improved upon coinfection with herpes simplex virus I thymidine kinase-carrying vectors that efficiently phosphorylate the antiviral drugs acyclovir or ganciclovir but not AZT or AZT-MP (6, 7).Therefore, we set out to understand the structural basis for the slow activation of AZT-MP. The structures of the yeast TmpK (TmpK yeast ) complexed with either the physiological substrate d...