Required for peroxisome biogenesis. Necessary for the developmental elimination of obsolete peroxisome matrix proteins. May be involved in the ubiquitination of PEX5, targeting it for recycling. Accepts the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine. Protein modification; protein ubiquitination. Interacts with PEX22. Belongs to the ubiquitin-conjugating enzyme family.