ATP-independent protease that degrades both mitochondrial and chloroplastic transit peptides after their cleavage. Also degrades other unstructured peptides. Specific for peptides in the range of 10 to 65 residues. Shows a preference for cleavage after small polar residues and before basic residues, but without any positional preference. Binds 1 zinc ion per subunit. Binds 2 Magnesium ions per subunit. Completely inhibited by the metal chelator orthophenanthroline. Homodimer. Expressed in leaves, flowers and roots, but not detected in siliques and shoots. Belongs to the peptidase M16 family. PreP subfamily.