Cloning and characterization of the novel d-aspartyl endopeptidase, paenidase, from Paenibacillus sp. B38

Paenidase is the first micro-organism-derived d-aspartyl endopeptidase that specifically recognizes an internal d-Asp residue to cleave [d-Asp]-X peptide bonds. Using peptide sequences obtained from the protein, we performed PCR with degenerate primers to amplify the paenidase I-encoding gene. Nucleotide Sequencing revealed that mature paenidase I consist of 322 amino acid residues and that the protein is encoded as a pro-protein with a 197-amino-acid N-terminal extension compared to the mature protein. Paenidase I exhibits amino acid sequence similarity to several penicillin-binding proteins. In addition, paenidase I was classified into peptidase family S12 based on a MEROPS database search. Family S12 contains serine-type d-Ala-d-Ala carboxypeptidases that have three active site residues (Ser, Lys and Tyr) in the conserved motifs Ser-Xaa-Thr-Lys and Tyr-Xaa-Asn. These motifs were conserved in the primary structure of paenidase I, and the role of these residues was confirmed by site-directed mutagenesis.