Metalloendopeptidase of the mitochondrial matrix that functions in peptide cleavage and degradation rather than in protein processing. Has an ATP-independent activity. Specifically cleaves peptides in the range of 5 to 65 residues. Shows a preference for cleavage after small polar residues and before basic residues, but without any positional preference. Degrades the transit peptides of mitochondrial proteins after their cleavage. Also degrades other unstructured peptides. It is also able to degrade amyloid-beta protein 40, one of the peptides produced by APP processing, when it accumulates in mitochondrion. It is a highly efficient protease, at least toward amyloid-beta protein 40. Cleaves that peptide at a specific position and is probably not processive, releasing digested peptides intermediates that can be further cleaved subsequently. It is also able to degrade amyloid-beta protein 42. Binds 1 zinc ion per subunit. Mainly exists in a closed and catalytically competent conformation but a closed-to-open switch allows substrate entry into the catalytic chamber. Substrate binding induces closure and dimerization. A disulfide bond may lock the enzyme in a closed conformation preventing substrate entry into the catalytic chamber, participating in redox regulation of the enzyme. Inhibited by metal-chelating agents. Inhibited by nickel and zinc excess, and slightly activated by manganese. Monomer and homodimer; homodimerization is induced by binding of the substrate. Up-regulated transplantes nuclei derived from embryonic stem (ES) cells. A disulfide bond locks the enzyme in the closed conformation preventing substrate entry into the catalytic chamber. Belongs to the peptidase M16 family. PreP subfamily. Truncated N-terminus.