Figure 1.

Interactions of the bisubstrate inhibitor with TmpK (a). Distance map of TP₅A bound to TmpK_coli. P loop residues are marked with an asterisk. (b–d) Stereoviews. Overlay of the TmpK_coli–TP₅A complex model (pink) with the TmpK_yeast–TP₅A model (green) (b and c) or the TmpK_coli–AZTP₅A (blue) (d). (b) Interactions of the 3′-hydroxyl of the thymidine deoxyribose. In TmpK_yeast, a bidentate interaction between the P loop aspartic acid and the sugar hydroxyl is observed. The binding of AZT-MP causes the P loop to move, thus displacing the catalytic P loop arginine. In contrast, in TmpK_coli, the interaction between Glu-12 and the 3′-hydroxyl is side-on, and the bulkier azido group does not induce a significant movement of the P loop. (c) Similar phosphate–arginine interactions made in TmpK_yeast by Arg-15 and in TmpK_coli by Arg-153. Displayed are the P loop and a part of the Lid region. The structures were overlaid according to the position of the bisubstrate inhibitor. (d) In the TmpK_coli–TP₅A and the TmpK_coli–AZTP₅A complex structures, the thymine base is at an identical position, but the deoxyribose moiety has undergone a rigid-body rotation caused by the azido group in the AZT-P₅A complex. In addition, Glu-12 has rotated slightly to provide more room for the azido group. The rotation of the deoxyribose induces a similar rotation of the Glu-160 side chain. As Glu-12 makes close interactions with Asp-157, the latter carboxylic acid also rotates slightly. b–d were generated by using bobscript (29, 30) and raster 3d (31).