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UniProtKB:Accession Number | Q9ZBA9 |
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Entry name | DAP_OCHAN |
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Activity | Release of an N-terminal D-amino acid from a peptide, Xaa-|-Yaa-, in which Xaa is preferably D-Ala, D-Ser or D- Thr. D-amino acid amides and methyl esters also are hydrolyzed, as is glycine amide. |
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Subunit | Homodimer. |
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Subcellular location |
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Cofactor |
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Compound table: links to PDB-related databases & PoSSuM |
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| Substrates | Products | intermediates |
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KEGG-id | C00012 | C00001 | C00012 | C00405 | I00087 | I00085 | I00086 |
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Compound | Peptide | H2O | Peptide | D-Amino acid | Peptidyl-tetrahedral intermediate | Acyl-enzyme | Tetrahedral intermediate |
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Type | peptide/protein | H2O | peptide/protein | amino acids |
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ChEBI |
| 15377
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PubChem |
| 962 22247451
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1ei5A01 |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | | | |
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1ei5A02 |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | | | |
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1ei5A03 |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | | | |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[9] | p.976 |
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references | [1] |
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PubMed ID | 2760064 |
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Journal | J Biol Chem |
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Year | 1989 |
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Volume | 264 |
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Pages | 14233-9 |
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Authors | Asano Y, Nakazawa A, Kato Y, Kondo K |
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Title | Properties of a novel D-stereospecific aminopeptidase from Ochrobactrum anthropi. |
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[2] |
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Journal | Tetrahedron |
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Year | 1989 |
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Volume | 45 |
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Pages | 5743-5754 |
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Authors | Kato Y, Asano Y, Nakazawa A, Kondo K |
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Title | First synthesis of D-amino acid N-alkyl amide catalyzed by D-aminopeptidase. |
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[3] |
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PubMed ID | 1540587 |
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Journal | Biochemistry |
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Year | 1992 |
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Volume | 31 |
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Pages | 2316-28 |
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Authors | Asano Y, Kato Y, Yamada A, Kondo K |
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Title | Structural similarity of D-aminopeptidase to carboxypeptidase DD and beta-lactamases. |
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Related UniProtKB | Q9ZBA9 |
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[4] |
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PubMed ID | 8439290 |
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Journal | Biochem J |
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Year | 1993 |
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Volume | 290 |
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Pages | 205-18 |
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Authors | Rawlings ND, Barrett AJ |
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Title | Evolutionary families of peptidases. |
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[5] |
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Journal | J Ferment Bioeng |
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Year | 1995 |
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Volume | 79 |
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Pages | 614-616 |
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Authors | Asano Y, Yamaguchi K |
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Title | Mutants of D-Aminopeptidase with Increased Thermal Stability |
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[6] |
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PubMed ID | 10379365 |
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Journal | Cell Mol Life Sci |
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Year | 1999 |
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Volume | 55 |
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Pages | 812-8 |
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Authors | Fanuel L, Thamm I, Kostanjevecki V, Samyn B, Joris B, Goffin C, Brannigan J, Van Beeumen J, Frere JM |
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Title | Two new aminopeptidases from Ochrobactrum anthropi active on D-alanyl-p-nitroanilide. |
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[7] |
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PubMed ID | 16232749 |
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Journal | J Biosci Bioeng |
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Year | 2000 |
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Volume | 89 |
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Pages | 295-306 |
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Authors | Asano Y, Lubbehusen TL |
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Title | Enzymes acting on peptides containing D-amino acid. |
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[8] |
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Journal | J Microbiol Biotechnol |
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Year | 2000 |
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Volume | 10 |
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Pages | 573-579 |
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Authors | Asano Y |
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Title | New enzymes acting on peptides containing D-Amino acids: Their properties and application. |
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[9] |
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PubMed ID | 10986464 |
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Journal | Structure Fold Des |
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Year | 2000 |
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Volume | 8 |
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Pages | 971-80 |
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Authors | Bompard-Gilles C, Remaut H, Villeret V, Prange T, Fanuel L, Delmarcelle M, Joris B, Frere J, Van Beeumen J |
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Title | Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family. |
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Related PDB | 1ei5 |
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[10] |
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Journal | J Mol Catal, B Enzym |
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Year | 2001 |
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Volume | 12 |
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Pages | 53?59 |
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Authors | Asano Y, Umezaki M, Li Y-F, Tsubota S, Lubbehusen TL |
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Title | Isolation of microorganisms which utilize acidic d-amino acid oligomers. |
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[11] |
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PubMed ID | 15913357 |
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Journal | J Am Chem Soc |
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Year | 2005 |
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Volume | 127 |
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Pages | 7696-7 |
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Authors | Asano Y, Yamaguchi S |
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Title | Dynamic kinetic resolution of amino acid amide catalyzed by D-aminopeptidase and alpha-amino-epsilon-caprolactam racemase. |
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[12] |
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PubMed ID | 16131658 |
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Journal | Protein Sci |
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Year | 2005 |
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Volume | 14 |
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Pages | 2296-303 |
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Authors | Delmarcelle M, Boursoit MC, Filee P, Baurin SL, Frere JM, Joris B |
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Title | Specificity inversion of Ochrobactrum anthropi D-aminopeptidase to a D,D-carboxypeptidase with new penicillin binding activity by directed mutagenesis. |
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comments | This enzyme belongs to peptidase family-S12. This enzyme has got a similar active site to that of its homologous enzyme, DD-carboxypeptidase (S00414 in EzCatDB). Thus, the catalytic mechanism can be similar to that of the homologous enzyme. According to the literature [9], the reaction of this enzyme probably proceeds as follows: (1) The pKa of Lys65 must be lowered (or modulated) by Tyr153 and Asn155. (2) Lys65 acts as a general base to activate Ser62. (3) Ser62 makes a nucleophilic attack on the target bond, leading to formation of tetrahedral intermediate. The intermediate should be stabilized by the mainchain amide groups of Ser62 and Ala290. (4) The second step involves the deacylation, which is the hydrolysis of the intermediate. According to the paper for its homologue (S00414 in EzCatDB), the phenoxide anion of Tyr153 would act as a general base, by activating a deacylating water for a nucleophile attack on the acyl-enzyme. Here, a positive charge on Lys65 would function as a modulator, by stabilzing the phenoxide anion on Tyr159, and by polarizing the ester bond for the nucleophilic attack by the water molecule (see S00414 in EzCatDB).
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created | updated |
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2006-01-24 | 2011-02-16 |
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