DB code: S00528

RLCP classification 1.13.30005.18 : Hydrolysis
CATH domain 3.60.70.12 : L-amino peptidase D-ALA esterase/amidase Catalytic domain
E.C. 3.4.11.19
CSA 1b65
M-CSA 1b65
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam
Q59632
D-aminopeptidase
EC 3.4.11.19
P01.001 (Mixed)
PF03576 (Peptidase_S58)
[Graphical View]

KEGG enzyme name
D-stereospecific aminopeptidase
D-aminopeptidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q59632 Q59632_OCHAN

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00012 C00001 C00012 C00133 C00405 I00087 I00085 I00086
E.C.
Compound Peptide H2O Peptide D-alanine D-Amino acid Peptidyl-tetrahedral intermediate Acyl-enzyme Tetrahedral intermediate
Type peptide/protein H2O peptide/protein amino acids amino acids
ChEBI 15377
15570
57416
PubChem 22247451
962
71080
7311725
1b65A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b65B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b65C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b65D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b65E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b65F Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b65A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 218;SER 250;SER 288 TYR 146;GLY 289
1b65B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 218;SER 250;SER 288 TYR 146;GLY 289
1b65C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 218;SER 250;SER 288 TYR 146;GLY 289
1b65D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 218;SER 250;SER 288 TYR 146;GLY 289
1b65E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 218;SER 250;SER 288 TYR 146;GLY 289
1b65F Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 218;SER 250;SER 288 TYR 146;GLY 289

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
Fig.5, p.2333-2334
[7]
Fig.7, p.159 5

References
[1]
Resource
Comments
Medline ID
PubMed ID 10089474
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 699-701
Authors Bompard-Gilles C, Villeret V, Fanuel L, Joris B, Frere JM, Van Beeumen J
Title Crystallization and preliminary X-ray analysis of a new L-aminopeptidase-D-amidase/D-esterase activated by a Gly-Ser peptide bond hydrolysis.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 10377256
Journal Biochem J
Year 1999
Volume 341
Pages 147-55
Authors Fanuel L, Goffin C, Cheggour A, Devreese B, Van Driessche G, Joris B, Van Beeumen J, Frere JM
Title The DmpA aminopeptidase from Ochrobactrum anthropi LMG7991 is the prototype of a new terminal nucleophile hydrolase family.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 10379365
Journal Cell Mol Life Sci
Year 1999
Volume 55
Pages 812-8
Authors Fanuel L, Thamm I, Kostanjevecki V, Samyn B, Joris B, Goffin C, Brannigan J, Van Beeumen J, Frere JM
Title Two new aminopeptidases from Ochrobactrum anthropi active on D-alanyl-p-nitroanilide.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 16232749
Journal J Biosci Bioeng
Year 2000
Volume 89
Pages 295-306
Authors Asano Y, Lubbehusen TL
Title Enzymes acting on peptides containing D-amino acid.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID
Journal J Microbiol Biotechnol
Year 2000
Volume 10
Pages 573-579
Authors Asano Y
Title New enzymes acting on peptides containing D-Amino acids: Their properties and application
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 11206054
Journal Protein Sci
Year 2000
Volume 9
Pages 2329-37
Authors Oinonen C, Rouvinen J
Title Structural comparison of Ntn-hydrolases.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY DIFFRACTION
Medline ID
PubMed ID 10673442
Journal Structure
Year 2000
Volume 8
Pages 153-62
Authors Bompard-Gilles C, Villeret V, Davies GJ, Fanuel L, Joris B, Frere JM, Van Beeumen J
Title A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.
Related PDB 1b65
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 15352873
Journal Biochem J
Year 2005
Volume 385
Pages 565-73
Authors Elkins JM, Kershaw NJ, Schofield CJ
Title X-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 15955066
Journal FEBS J
Year 2005
Volume 272
Pages 3075-84
Authors Komeda H, Asano Y
Title A DmpA-homologous protein from Pseudomonas sp. is a dipeptidase specific for beta-alanyl dipeptides.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 15937278
Journal Protein Sci
Year 2005
Volume 14
Pages 1902-10
Authors Cheng H, Grishin NV
Title DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to peptidase family-S58.
Although this enzyme is synthesized as a single polypeptide, the active form consists of two peptides made from the cleavage of the Gly249-Ser250 peptide bond (see [7]). The N-terminal alpha-amine group of Ser250 is extremely important as a general base. Thus, the catalytic mechanism of this enzyme is compared with those of N-terminal nucleophile (Ntn) hydrolases such as proteasome (M00123, M00174 in EzCatDB). The structural topology of this enzyme is distinct from the Ntn hydrolase superfamily (CATH 3.60.20.10).
According to the literature [7], the catalytic reaction proceeds as follows:
(1) Ser288 modulates the activity of the alpha-amine group of Ser250, whereas mainchain amide of Gly289 modulates the sidechain of Ser250.
(2) The alpha-amine group acts as a general base to deprotonate and activate the sidechain hydroxyl group of Ser250.
(3) The activated Ser250 makes a nucleophilic attack on the carbonyl carbon of the substrate, leading to the formation of a tetrahedral transition-state. The transition-state is stabilized by an oxyanion hole, composed of the sidechain amide of Asn218 and mainchain amide of Tyr146.
(4) The alpha-amine group acts as a general acid to protonate the leaving amine group, leading to the acyl-enzyme intermediate.
(5) The alpha-amine group acts as a general base to deprotonate and activate the hydrolytic water.
(6) The activated water makes a nucleophilic attack on the carbonyl carbon of the acyl-enzyme intermediate, leading to the formation of a tetrahedral transition-state again. The transition-state is stabilized by the oxyanion hole.
(7) The alpha-amine group acts as a general acid to protonate the leaving amine group, completing the reaction.

Created Updated
2006-01-24 2011-02-16