title: A Porphyromonas gingivalis Periplasmic Novel Exopeptidase, Acylpeptidyl Oligopeptidase, Releases N-Acylated Di- and Tripeptides from Oligopeptides.
abstract: Exopeptidases, including dipeptidyl- and tripeptidylpeptidase, are crucial for the growth of Porphyromonas gingivalis, a periodontopathic asaccharolytic bacterium that incorporates amino acids mainly as di- and tripeptides. In this study, we identified a novel exopeptidase, designated acylpeptidyl oligopeptidase (AOP), composed of 759 amino acid residues with active Ser(615) and encoded by PGN_1349 in P. gingivalis ATCC 33277. AOP is currently listed as an unassigned S9 family peptidase or prolyl oligopeptidase. Recombinant AOP did not hydrolyze a Pro-Xaa bond. In addition, although sequence similarities to human and archaea-type acylaminoacyl peptidase sequences were observed, its enzymatic properties were apparently distinct from those, because AOP scarcely released an N-acyl-amino acid as compared with di- and tripeptides, especially with N-terminal modification. The kcat/Km value against benzyloxycarbonyl-Val-Lys-Met-4-methycoumaryl-7-amide, the most potent substrate, was 123.3 ± 17.3 μm(-1) s(-1), optimal pH was 7-8.5, and the activity was decreased with increased NaCl concentrations. AOP existed predominantly in the periplasmic fraction as a monomer, whereas equilibrium between monomers and oligomers was observed with a recombinant molecule, suggesting a tendency of oligomerization mediated by the N-terminal region (Met(16)-Glu(101)). Three-dimensional modeling revealed the three domain structures (residues Met(16)-Ala(126), which has no similar homologue with known structure; residues Leu(127)-Met(495) (β-propeller domain); and residues Ala(496)-Phe(736) (α/β-hydrolase domain)) and further indicated the hydrophobic S1 site of AOP in accord with its hydrophobic P1 preference. AOP orthologues are widely distributed in bacteria, archaea, and eukaryotes, suggesting its importance for processing of nutritional and/or bioactive oligopeptides.
authors.affiliation: From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan.
authors.forename: Takayuki K
authors.initials: TK
authors.lastname: Nemoto
authors.affiliation: From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Ohara-Nemoto
authors.affiliation: the Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria, and. Electronic address: tnemoto@nagasaki-u.ac.jp.
authors.forename: Gustavo Arruda
authors.initials: GA
authors.lastname: Bezerra
authors.affiliation: the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shimoyama
authors.affiliation: the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, Japan.
authors.forename: Shigenobu
authors.initials: S
authors.lastname: Kimura
mesh_terms: D000215:Acylation; D000595:Amino Acid Sequence; D016866:Bacteroidaceae Infections / Q000382:microbiology*; D020689:Exopeptidases / Q000032:analysis / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism*; D010447:Peptide Hydrolases / Q000032:analysis / Q000378:metabolism*; D016966:Porphyromonas gingivalis / Q000737:chemistry / Q000166:cytology / Q000201:enzymology* / Q000378:metabolism; D011487:Protein Conformation; D055503:Protein Multimerization
chemical_list: D009842:Oligopeptides; D020689:Exopeptidases; D010447:Peptide Hydrolases; C028759:oligopeptidase; C038220:acylaminoacyl-peptidase
keywords: DFP-6; acylaminoacyl peptidase; aminopeptidase; microbial pathogenesis; oligomerization; oligopeptidase B; peptidase; periodontal disease