EzCatDB: S00406
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DB codeS00406
RLCP classification1.13.11400.1261 : Hydrolysis
CATH domainDomain 13.40.630.10 : AminopeptidaseCatalytic domain
E.C.3.4.11.10
CSA1amp

CATH domainRelated DB codes (homologues)
3.40.630.10 : AminopeptidaseD00512,S00407,D00192,D00193,D00467

Enzyme Name
UniProtKBKEGG

Q01693
Protein nameBacterial leucyl aminopeptidasebacterial leucyl aminopeptidase
Aeromonas proteolytica aminopeptidase
SynonymsEC 3.4.11.10
MEROPSM28.002 (Metallo)
PfamPF04389 (Peptidase_M28)
PF04151 (PPC)
[Graphical view]


UniProtKB:Accession NumberQ01693
Entry nameAMPX_VIBPR
ActivityRelease of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.
Subunit
Subcellular locationSecreted.
CofactorBinds 2 zinc ions per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00038C00017C00012C00001C00017C00012C00123
CompoundZincProteinPeptideH2OProteinPeptideL-Leucine
Typeheavy metalpeptide/proteinpeptide/proteinH2Opeptide/proteinpeptide/proteinamino acids
ChEBI29105


15377


15603
57427

PubChem32051


962
22247451


7045798
6106

                
1ampABound:2x_ZNUnboundUnbound UnboundUnboundUnboundUnbound
1cp6ABound:2x_ZNUnboundUnbound UnboundUnboundUnboundTransition-state-analogue:BUB
1ft7ABound:2x_ZNUnboundUnbound UnboundUnboundAnalogue:PLUUnbound
1igbABound:2x_ZNUnboundUnbound UnboundUnboundAnalogue:IPOUnbound

Active-site residues
resource
Swiss-prot;Q01693
pdbCatalytic residuesCofactor-binding residues
          
1ampAGLU 151
HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1cp6AGLU 151
HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1ft7AGLU 151
HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1igbAGLU 151
HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.396-397
[5]Fig.7, p.4283-42854
[6]p.9050-9053
[10]Fig.10, p.7042-70454
[12]p.1196-1199

references
[1]
PubMed ID8357796
JournalBiochemistry
Year1993
Volume32
Pages8465-78
AuthorsKim H, Lipscomb WN
TitleX-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state.
[2]
CommentsX-ray crystallography (1.8 Angstroms)
Medline ID94373500
PubMed ID8087555
JournalStructure
Year1994
Volume2
Pages283-91
AuthorsChevrier B, Schalk C, D'Orchymont H, Rondeau JM, Moras D, Tarnus C
TitleCrystal structure of Aeromonas proteolytica aminopeptidase: a prototypical member of the co-catalytic zinc enzyme family.
Related PDB1amp
Related UniProtKBQ01693
[3]
PubMed ID7578088
JournalBiochemistry
Year1995
Volume34
Pages14792-800
AuthorsStrater N, Lipscomb WN
TitleTwo-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography.
[4]
CommentsX-ray crystallography complex with inhibitor
Medline ID96215434
PubMed ID8647077
JournalEur J Biochem
Year1996
Volume237
Pages393-8
AuthorsChevrier B, D'Orchymont H, Schalk C, Tarnus C, Moras D
TitleThe structure of the Aeromonas proteolytica aminopeptidase complexed with a hydroxamate inhibitor. Involvement in catalysis of Glu151 and two zinc ions of the co-catalytic unit.
Related PDB1igb
Related UniProtKBQ01693
[5]
Commentsmechanistic studies, catalysis
PubMed ID9100023
JournalBiochemistry
Year1997
Volume36
Pages4278-86
AuthorsChen G, Edwards T, D'souza VM, Holz RC
TitleMechanistic studies on the aminopeptidase from Aeromonas proteolytica: a two-metal ion mechanism for peptide hydrolysis.
[6]
CommentsX-ray crystallography (1.9 Angstroms)
PubMed ID10413478
JournalBiochemistry
Year1999
Volume38
Pages9048-53
AuthorsDe Paola CC, Bennett B, Holz RC, Ringe D, Petsko GA
Title1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development.
Related PDB1cp6
[7]
Commentsinhibition, catalysis
PubMed ID10471294
JournalBiochemistry
Year1999
Volume38
Pages11433-9
AuthorsUstynyuk L, Bennett B, Edwards T, Holz RC
TitleInhibition of the aminopeptidase from Aeromonas proteolytica by aliphatic alcohols. Characterization of the hydrophobic substrate recognition site.
[8]
PubMed ID10500145
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages11151-5
AuthorsStrater N, Sun L, Kantrowitz ER, Lipscomb WN
TitleA bicarbonate ion as a general base in the mechanism of peptide hydrolysis by dizinc leucine aminopeptidase.
[9]
Commentsinhibition
PubMed ID10569943
JournalBiochemistry
Year1999
Volume38
Pages15587-96
AuthorsHuntington KM, Bienvenue DL, Wei Y, Bennett B, Holz RC, Pei D
TitleSlow-binding inhibition of the aminopeptidase from Aeromonas proteolytica by peptide thiols: synthesis and spectroscopic characterization.
[10]
CommentsX-ray crystallography (2.1 Angstroms)
PubMed ID11401547
JournalBiochemistry
Year2001
Volume40
Pages7035-46
AuthorsStamper C, Bennett B, Edwards T, Holz RC, Ringe D, Petsko G
TitleInhibition of the aminopeptidase from Aeromonas proteolytica by L-leucinephosphonic acid. Spectroscopic and crystallographic characterization of the transition state of peptide hydrolysis.
Related PDB1ft7
[11]
CommentsX-ray crystallography (1.53-1.80 Angstroms)
PubMed ID11484227
JournalProteins
Year2001
Volume44
Pages490-504
AuthorsGilboa R, Spungin-Bialik A, Wohlfahrt G, Schomburg D, Blumberg S, Shoham G
TitleInteractions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism.
[12]
PubMed ID11743734
JournalJ Mol Biol
Year2001
Volume314
Pages1191-207
AuthorsWouters MA, Husain A
TitleChanges in zinc ligation promote remodeling of the active site in the zinc hydrolase superfamily.

comments
This enzyme belongs to the peptidase family-M28A.
The paper [4] suggested that Glu151 could play the catalytic role as a general base in the catalysis.
According to the literature [5], as for the metal-bound water, the higher the coordination number, the higher the pKa. Furthermore, as the number of carboxylate ligands to a Zn(II) ion increases, the pKa becomes the higher [5]. Thus, Glu151 facilitate the deprotonation of the terminal water molecule to the nucleophilic hydroxo moiety, which can attack the activated scissile carbonyl carbon of the peptide substrate, forming a gem-diolate intermediate complex that is stabilized by coordination of both oxygen atoms to the dizinc(II) center. In addition, at the next stage, Glu151 can donate an additional proton to the penultimate amino nitrogen recovering its ionized state.
According to the paper [12], the transition state is a non-covalently bound tetrahedral gem-diolate, which is opposed to a covalent acyl anhydride transition state as found in serine proteases.

createdupdated
2002-09-272009-02-26
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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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