ATP-dependent serine protease that mediates the selective degradation of misfolded and unassembled polypeptides in the peroxisomal matrix. Necessary for type 2 peroxisome targeting signal (PTS2)-containing protein processing and facilitates peroxisome matrix protein import. May indirectly regulate peroxisomal fatty acid beta-oxidation through degradation of the self-processed forms of TYSND1. Hydrolysis of proteins in presence of ATP. Interacts with PEX5. Interacts with TYSND1 (By similarity). May interact with enzymes involved in beta-oxidation of fatty acids, including ACOX1/AOX (By similarity). Belongs to the peptidase S16 family.