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, with a bias for positively charged amino acid residues. Binds 1 zinc ion per subunit. Binds 2 Magnesium ions per subunit. Inactive in the absence of MgCl(2) and CaCl(2) and full activation at 10 mM concentrations of either ion. Completely inhibited by the metal chelator orthophenanthroline, but not affected by phenylmethylsulfonyl fluoride (PMSF) or N-ethylmaleimide (NEM). Active from pH 4 to 10. Optimum temperature is 28 degrees Celsius. Active from 4 to 40 degrees Celsius. Homodimer. A number of isoforms are produced. According to EST sequences. Expressed only in siliques and flowers. The 2 enzymes halves enclose a large proteolytic chamber spacious enough to hold peptide substrates, but sufficiently small to exclude larger, folded proteins. Since the active site includes residues from both the N- and C-terminal part of the protein, proteolysis can occur only when the chamber is closed. Covalently locking the 2 halves of the protease with disulfide bonds induces a loss of activity. Belongs to the peptidase M16 family. PreP subfamily.