EzCatDB: S00528

DB codeS00528
RLCP classification1.13.30005.18
CATH domainDomain 13.60.70.12Catalytic domain
E.C.3.4.11.19
CSA1b65


Enzyme Name
Swiss-protKEGG

Q59632
Protein name
D-stereospecific aminopeptidase
D-aminopeptidase
SynonymsD-aminopeptidase
EC 3.4.11.19


Swiss-prot:Accession NumberQ59632
Entry nameQ59632_OCHAN
Activity
Subunit
Subcellular location
Cofactor


SubstratesProductsintermediates
KEGG-idC00012C00001C00012C00133C00405I00087I00085I00086
CompoundPeptideH2OPeptideD-alanineD-Amino acidPeptidyl-tetrahedral intermediateAcyl-enzymeTetrahedral intermediate
Typepeptide/proteinH2Opeptide/proteinamino acidsamino acids


1b65AUnbound
UnboundUnboundUnbound


1b65BUnbound
UnboundUnboundUnbound


1b65CUnbound
UnboundUnboundUnbound


1b65DUnbound
UnboundUnboundUnbound


1b65EUnbound
UnboundUnboundUnbound


1b65FUnbound
UnboundUnboundUnbound



Active-site residues
resource
literature [7]
pdbCatalytic residuesMain-chain involved in catalysis
1b65AASN 218;SER 250;SER 288
TYR 146;GLY 289
1b65BASN 218;SER 250;SER 288
TYR 146;GLY 289
1b65CASN 218;SER 250;SER 288
TYR 146;GLY 289
1b65DASN 218;SER 250;SER 288
TYR 146;GLY 289
1b65EASN 218;SER 250;SER 288
TYR 146;GLY 289
1b65FASN 218;SER 250;SER 288
TYR 146;GLY 289

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]Fig.5, p.2333-2334
[7]Fig.7, p.1595

references
[1]
PubMed ID10089474
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages699-701
AuthorsBompard-Gilles C, Villeret V, Fanuel L, Joris B, Frere JM, Van Beeumen J
TitleCrystallization and preliminary X-ray analysis of a new L-aminopeptidase-D-amidase/D-esterase activated by a Gly-Ser peptide bond hydrolysis.
[2]
PubMed ID10377256
JournalBiochem J
Year1999
Volume341
Pages147-55
AuthorsFanuel L, Goffin C, Cheggour A, Devreese B, Van Driessche G, Joris B, Van Beeumen J, Frere JM
TitleThe DmpA aminopeptidase from Ochrobactrum anthropi LMG7991 is the prototype of a new terminal nucleophile hydrolase family.
[3]
PubMed ID10379365
JournalCell Mol Life Sci
Year1999
Volume55
Pages812-8
AuthorsFanuel L, Thamm I, Kostanjevecki V, Samyn B, Joris B, Goffin C, Brannigan J, Van Beeumen J, Frere JM
TitleTwo new aminopeptidases from Ochrobactrum anthropi active on D-alanyl-p-nitroanilide.
[4]
PubMed ID16232749
JournalJ Biosci Bioeng
Year2000
Volume89
Pages295-306
AuthorsAsano Y, Lubbehusen TL
TitleEnzymes acting on peptides containing D-amino acid.
[5]
JournalJ Microbiol Biotechnol
Year2000
Volume10
Pages573-579
AuthorsAsano Y
TitleNew enzymes acting on peptides containing D-Amino acids: Their properties and application
[6]
PubMed ID11206054
JournalProtein Sci
Year2000
Volume9
Pages2329-37
AuthorsOinonen C, Rouvinen J
TitleStructural comparison of Ntn-hydrolases.
[7]
CommentsX-RAY DIFFRACTION
PubMed ID10673442
JournalStructure
Year2000
Volume8
Pages153-62
AuthorsBompard-Gilles C, Villeret V, Davies GJ, Fanuel L, Joris B, Frere JM, Van Beeumen J
TitleA new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.
Related PDB1b65
[8]
PubMed ID15352873
JournalBiochem J
Year2005
Volume385
Pages565-73
AuthorsElkins JM, Kershaw NJ, Schofield CJ
TitleX-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster.
[9]
PubMed ID15955066
JournalFEBS J
Year2005
Volume272
Pages3075-84
AuthorsKomeda H, Asano Y
TitleA DmpA-homologous protein from Pseudomonas sp. is a dipeptidase specific for beta-alanyl dipeptides.
[10]
PubMed ID15937278
JournalProtein Sci
Year2005
Volume14
Pages1902-10
AuthorsCheng H, Grishin NV
TitleDOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.

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.

createdupdated
2006-01-242011-02-16
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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