HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP(5)A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER

The structure of adenylate kinase from yeast ligated with the two-subs trate-mimicking inhibitor Ap(5)A and Mg2+ has been refined to 1.96 Ang strom resolution. In addition, the refined structure of the same compl ex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 Angstrom. These structures indicate that replacing Mg2+ by imi dazole disturbs the water structure and thus the complex. A comparison with the G-proteins shows that Mg2+ is exactly at the same position w ith respect to the phosphates. However, although the Mg2+ ligand spher e of the G-proteins is a regular octahedron containing peptide ligands , the reported adenylate kinase has no such ligands and an open octahe dron leaving space for the Mg2+ to accompany the transferred phosphory l group. A superposition of the known crystalline and therefore pertur bed phosphoryl transfer geometries in the adenylate kinases demonstrat es that all of them are close to the start of the forward reaction wit h bound ATP and AMP. Averaging all observed perturbed structures gives rise to a close approximation of the transition state, indicating in general how to establish an elusive transition state geometry. The ave rage shows that the in-line phosphoryl transfer is associative, becaus e there is no space for a dissociative metaphosphate intermediate. As a side result, the secondary dipole interaction in the alpha-helices o f both protein structures has been quantified.