Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, but is not implicated in protein degradation by the 26S proteasome, deneddylation, or desumoylation. Required for intracellular trafficking (e.g. trafficking from the Golgi to the vacuole and the vacuolar trafficking of endocytosed cargo), endocytosis and vacuole biogenesis. Binds 2 Zn(2+) ions per subunit. Interacts with PATL1 and PATL2. May also bind to HSC70-1, HSC70-3, VHA-A, BGLU23 and EPSIN1. Interacts with BRO1/ALIX (PubMed:26324913). Localized in late endosome when associated with BRO1/ALIX. The JAMM motif is essential for the protease activity. Seedling growth arrest phenotype. Impaired central lytic vacuole formation, autophagosomes accumulation, and mis-sorting of vacuolar protein cargo to the intercellular space as well as disturbed endocytosis. Belongs to the peptidase M67C family.