Structural similarity of D-aminopeptidase to carboxypeptidase DD and beta-lactamases

The gene for D-aminopeptidase (dap) has been isolated from the bacterium Ochrobactrum anthropi SCRC C1-38 [Asano, Y., Nakazawa, A., Kato, Y., & Kondo, K. (1989) J. Biol. Chem. 264, 14233-14239] and its nucleotide sequence determined. An expression plasmid pC138DP (4.5 kb) was constructed by placing the gene downstream of the lac promoter of pUC19. The amount of the enzyme in the cell-free extract of Escherichia coli JM109/pC138DP was elevated to 288,000 units/L of culture, which is about 3600-fold over that of O. anthropi SCRC C1-38. The enzyme comprised about 30% of the total extractable cellular protein. The gene consisted of an open reading frame of 1560 nucleotides which specifies a protein of Mr 57,257. The deduced amino acid sequence of the enzyme showed that it is related to carboxypeptidase DD, beta-lactamases, and penicillin-binding proteins. Seven mutants of the enzyme were generated by site-specific mutagenesis to explore the roles of the residues of interest, around the sequence Ser61-Xaa-Xaa-Lys64, where Xaa is any amino acid, since the identical sequences also appear in the penicillin-recognizing peptide hydrolases with Ser at the active sites. The mutant enzymes expressed in E. coli were purified to homogeneity and kinetically characterized. Replacements of the site at Ser61 and Lys64 yielded mutants showing significantly reduced Vmax values, while most of the Km values remained unchanged. Changes at Cys60, which is adjacent to the likely active center Ser61, to Ser and Gly resulted in the production of enzyme less sensitive to PCMB, with almost unaltered Vmax/Km values. The enzyme appears to be a serine peptidase rather than a thiol one. The inhibition by PCMB in the wild-type enzyme may have been caused by a formation of a mercaptide bond between Cys 60 and PCMB. Considering that D-aminopeptidase, carboxypeptidase DD (a penicillin-binding protein), and beta-lactamase have a common feature in recognizing peptides containing D-amino acid and that the former two catalyze transpeptidation reactions with substrates containing D-alanyl-D-alanine moieties, we propose that the enzyme is a new member of the "penicillin-recognizing enzymes". We showed that the enzyme is actually inhibited by beta-lactam compounds, such as 6-APA, 7-ACA, benzylpenicillin, and ampicillin, although they are not the substrate for the enzyme. The relationship between the primary structures and the reactions catalyzed by D-aminopeptidase and other serine hydrolases beta-lactamases and carboxypeptidase DD is discussed.(ABSTRACT TRUNCATED AT 400 WORDS)