DB code: T00222

RLCP classification	1.13.30015.15 : Hydrolysis
CATH domain	3.40.710.10 : Beta-lactamase	Catalytic domain
	2.40.128.50 : Lipocalin
	2.40.128.50 : Lipocalin
E.C.	3.4.11.19
CSA	1ei5
M-CSA	1ei5
MACiE

CATH domain	Related DB codes (homologues)
3.40.710.10 : Beta-lactamase	S00512 S00513 S00529 S00414

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	MEROPS	Pfam
Q9ZBA9	D-aminopeptidase	EC 3.4.11.19	S12.002 (Serine)	PF00144 (Beta-lactamase) PF07930 (DAP_B) PF07932 (DAP_C) [Graphical View]

KEGG enzyme name
D-stereospecific aminopeptidase D-aminopeptidase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
Q9ZBA9	DAP_OCHAN	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.	Homodimer.

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates		Products		Intermediates
KEGG-id	C00012	C00001	C00012	C00405	I00087	I00085	I00086
E.C.
Compound	Peptide	H2O	Peptide	D-Amino acid	Peptidyl-tetrahedral intermediate	Acyl-enzyme	Tetrahedral intermediate
Type	peptide/protein	H2O	peptide/protein	amino acids
ChEBI		15377
PubChem		962 22247451

1ei5A01	Unbound		Unbound	Unbound
1ei5A02	Unbound		Unbound	Unbound
1ei5A03	Unbound		Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
literature [9]

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1ei5A01	SER 62;LYS 65;TYR 153;HIS 287			SER 62;ALA 290
1ei5A02
1ei5A03

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[9]	p.976

References
[1]
Resource
Comments
Medline ID
PubMed ID	2760064
Journal	J Biol Chem
Year	1989
Volume	264
Pages	14233-9
Authors	Asano Y, Nakazawa A, Kato Y, Kondo K
Title	Properties of a novel D-stereospecific aminopeptidase from Ochrobactrum anthropi.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID
Journal	Tetrahedron
Year	1989
Volume	45
Pages	5743-5754
Authors	Kato Y, Asano Y, Nakazawa A, Kondo K
Title	First synthesis of D-amino acid N-alkyl amide catalyzed by D-aminopeptidase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	1540587
Journal	Biochemistry
Year	1992
Volume	31
Pages	2316-28
Authors	Asano Y, Kato Y, Yamada A, Kondo K
Title	Structural similarity of D-aminopeptidase to carboxypeptidase DD and beta-lactamases.
Related PDB
Related UniProtKB	Q9ZBA9
[4]
Resource
Comments
Medline ID
PubMed ID	8439290
Journal	Biochem J
Year	1993
Volume	290
Pages	205-18
Authors	Rawlings ND, Barrett AJ
Title	Evolutionary families of peptidases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID
Journal	J Ferment Bioeng
Year	1995
Volume	79
Pages	614-616
Authors	Asano Y, Yamaguchi K
Title	Mutants of D-Aminopeptidase with Increased Thermal Stability
Related PDB
Related UniProtKB
[6]
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
[7]
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
[8]
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
[9]
Resource
Comments
Medline ID
PubMed ID	10986464
Journal	Structure Fold Des
Year	2000
Volume	8
Pages	971-80
Authors	Bompard-Gilles C, Remaut H, Villeret V, Prange T, Fanuel L, Delmarcelle M, Joris B, Frere J, Van Beeumen J
Title	Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.
Related PDB	1ei5
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID
Journal	J Mol Catal, B Enzym
Year	2001
Volume	12
Pages	53?59
Authors	Asano Y, Umezaki M, Li Y-F, Tsubota S, Lubbehusen TL
Title	Isolation of microorganisms which utilize acidic d-amino acid oligomers.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	15913357
Journal	J Am Chem Soc
Year	2005
Volume	127
Pages	7696-7
Authors	Asano Y, Yamaguchi S
Title	Dynamic kinetic resolution of amino acid amide catalyzed by D-aminopeptidase and alpha-amino-epsilon-caprolactam racemase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID	16131658
Journal	Protein Sci
Year	2005
Volume	14
Pages	2296-303
Authors	Delmarcelle M, Boursoit MC, Filee P, Baurin SL, Frere JM, Joris B
Title	Specificity inversion of Ochrobactrum anthropi D-aminopeptidase to a D,D-carboxypeptidase with new penicillin binding activity by directed mutagenesis.
Related PDB
Related UniProtKB

Comments
(2) Lys65 acts as a general base to activate Ser62. 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. (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).

Comments

(2) Lys65 acts as a general base to activate Ser62.
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.
(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).

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