Required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. It is thought that this protein is a protease that cleaves peptides bond in a small peptide (gene pqqA), providing the glutamate and tyrosine residues which are necessary for the synthesis of PQQ. Binds 1 zinc ion per subunit. Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Belongs to the peptidase M16 family.