title: Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis.
abstract: The crystal structure of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis was determined. Prolyl tripeptidyl aminopeptidase consists of beta-propeller and catalytic domains, and a large cavity between the domains; this structure is similar to dipeptidyl aminopeptidase IV. A catalytic triad (Ser603, His710, and Asp678) was located in the catalytic domain; this triad was virtually identical to that of the enzymes belonging to the prolyl oligopeptidase family. The structure of an inactive S603A mutant enzyme complexed with a substrate was also determined. The pyrrolidine ring of the proline residue appeared to fit into a hydrophobic pocket composed of Tyr604, Val629, Trp632, Tyr635, Tyr639, Val680, and Val681. There were characteristic differences in the residues of the beta-propeller domain, and these differences were related to the substrate specificity of tripeptidyl activity. The N-terminal amino group was recognized by salt bridges, with two carboxyl groups of Glu205 and Glu206 from a helix in dipeptidyl aminopeptidase IV. In prolyl tripeptidyl aminopeptidase, however, the Glu205 (located in the loop) and Glu636 were found to carry out this function. The loop structure provides sufficient space to accommodate three N-terminal residues (Xaa-Xaa-Pro) of substrates. This is the first report of the structure and substrate recognition mechanism of tripeptidyl peptidase.
authors.affiliation: Gradute School of Biomedical Sciences, Nagasaki University 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Ito
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Nakajima
authors.forename: Yue
authors.initials: Y
authors.lastname: Xu
authors.forename: Nozomi
authors.initials: N
authors.lastname: Yamada
authors.forename: Yuko
authors.initials: Y
authors.lastname: Onohara
authors.forename: Takashi
authors.initials: T
authors.lastname: Ito
authors.forename: Futoshi
authors.initials: F
authors.lastname: Matsubara
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Kabashima
authors.forename: Koji
authors.initials: K
authors.lastname: Nakayama
authors.forename: Tadashi
authors.initials: T
authors.lastname: Yoshimoto
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002417:Cattle; D018360:Crystallography, X-Ray; D004152:Dipeptidyl-Peptidases and Tripeptidyl-Peptidases; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D016297:Mutagenesis, Site-Directed; D016966:Porphyromonas gingivalis / Q000201:enzymology*; D020836:Protein Structure, Quaternary; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013552:Swine
chemical_list: D001426:Bacterial Proteins; D021122:Protein Subunits; D004152:Dipeptidyl-Peptidases and Tripeptidyl-Peptidases; C118449:PtpA protein, Porphyromonas gingivalis; D012697:Serine Endopeptidases