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 15377		15570 57416 15570 57416
PubChem		22247451 962 22247451 962		71080 7311725 71080 7311725

1b65A	Unbound		Unbound	Unbound	Unbound
1b65B	Unbound		Unbound	Unbound	Unbound
1b65C	Unbound		Unbound	Unbound	Unbound
1b65D	Unbound		Unbound	Unbound	Unbound
1b65E	Unbound		Unbound	Unbound	Unbound
1b65F	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	ASN 218;SER 250;SER 288			TYR 146;GLY 289
1b65B	ASN 218;SER 250;SER 288			TYR 146;GLY 289
1b65C	ASN 218;SER 250;SER 288			TYR 146;GLY 289
1b65D	ASN 218;SER 250;SER 288			TYR 146;GLY 289
1b65E	ASN 218;SER 250;SER 288			TYR 146;GLY 289
1b65F	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.

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