Figure 3: Substrate-binding sites of DgkA.

(a) Binding of the adenosine of ACP at the extracellular surface of active site asBC. Interactions are shown as dashed lines with distances between non-hydrogen atoms in Å. Protein and ACP carbons are coloured green and yellow, respectively. Oxygen and nitrogen are coloured red and blue, respectively. (b) Binding of the zinc-triphosphate moiety of zinc-ACP to asBC. Lipid carbons are coloured black. Distances for zinc coordination range from 2.0 to 2.2 Å. The asterisks indicate that little or no electron density was observed for the side chains of Arg9 and Glu28. However, interactions with zinc-ACP, of the type noted, were seen with both residues in MDS (Supplementary Movie 1). (c) The putative active site of DgkA where the catalytic residue Glu69_C, ACP and lipid substrate MAG1 meet in asBC. The glycerol headgroup of MAG1 could not be oriented unambiguously in the active site based on the available electron density maps, even at 2.05 Å resolution (Supplementary Fig. 4a–d). Accordingly, the interactions between MAG1 and the enzyme are shown as dashed lines only and without specifying distances. The orientation shown, with the 1-OH in hydrogen-bonding distance to the carboxyl group of Glu69, is plausible in light of a careful consideration of the available maps and the nature of the lipid substrate and the reaction being catalysed.