Catalysis of the transfer of Pup to a substrate protein via the reaction X-Pup + S = X + S-Pup, where X is either an E2 or E3 enzyme, the X-Pup linkage is a thioester bond, and the S-Pup linkage is an isopeptide bond between the C-terminal amino acid of Pup and the epsilon-amino group of lysine residues in the substrate.
E3