The pupylation/depupylation cycle in mycobacteria. Dop (green) renders PupQ ligation-competent by deamidating the carboxy-terminal glutamine to glutamate. The Pup ligase PafA (blue) then performs the isopeptide-bond formation between the γ-carboxylate of Pup's carboxy-terminal glutamate and the ε-amino group of a substrate (grey). Dop also carries out the specific cleavage of the isopeptide-bond in a pupylated substrate, depupylating the tagged substrate protein. Pup (red) has been placed in the proposed Pup-binding groove of Dop or PafA with its carboxy-terminal residue pointing into the active site.