Dop and PafA are close structural homologs but catalyze distinct reactions. (a,b) The structures of Dop (a) and PafA (b) are shown in cartoon representation with ATP/ADP displayed in stick format. The catalyzed reactions are shown below the corresponding enzyme. For deamidation, R denotes a hydrogen; for depupylation or ligation, R denotes the protein lysyl moiety. Pup (dotted red line) is represented as binding in the putative Pup-binding groove with its carboxy-terminal glutamate (red, sticks) placed in the active site according to the position of glutamate in glutamyl-cysteine ligase (PDB: 2gwd). In PafA, Pup is displayed in its activated form corresponding to the phosphorylated intermediate shown in the scheme below (Pi is indicated by a red sphere).
Barandun et al. BMC Biology 2012 10:95 doi:10.1186/1741-7007-10-95