Figure 4: Changes in the active site of the DgkA ternary complex at the beginning and end of a 100-ns MDS.

(a) WT simulation of ATP based on the ACP coordinates. There are limited differences in the binding site between the start (grey) and end (colour) of the MDS. (b) E28A mutation (red). This principally affects the binding of the Zn2 ion. In the absence of the E28 side chain the zinc ions become purely coordinated by E76 and the ATP phosphates. As a result, the entire zinc-ATP complex moves away from the protein, towards the cytoplasm. This, in turn, slightly alters the conformation of the CL. (c) E76A (red). To compensate for the loss of E76, the zinc ions move towards the membrane to interact with E69. This pulls the ATP in the same direction and, in turn, the CL is affected. (d) K94A (red). The WT residue coordinates both α-phosphate and N7 of the adenine ring of ATP. The loss of the basic side-chain releases the adenine of ATP and the binding is lost. In WT simulations, K94 forms a salt bridge with D80 and it is expected that the loss of this bridge in the D80A mutant can also explain the loss of catalytic ability in this mutant. (e) GTP. The major difference in dynamics is observed in the CL, where the loss of the N6 hydrogen bond with the backbone of E85 destabilizes purine binding and the CL. (f) ADP. The ADP molecule is expected to leave the binding site after catalysis has taken place. A change in zinc ion coordination takes place as Zn1 now coordinates the α- and β-phosphates of ADP. This relocates ADP closer to K94, which also coordinates both phosphates. In turn, K94 no longer interacts with the N7 position of the purine ring, which changes conformation, priming the ADP molecule for exit. Throughout this legend, WT refers to Δ4-DgkA (ref. 12).