DB code: S00406

RLCP classification 1.13.11400.1261 : Hydrolysis
CATH domain 3.40.630.10 : Aminopeptidase Catalytic domain
E.C. 3.4.11.10
CSA 1amp
M-CSA 1amp
MACiE

CATH domain Related DB codes (homologues)
3.40.630.10 : Aminopeptidase D00512 S00407 D00192 D00193 D00467

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam
Q01693 Bacterial leucyl aminopeptidase
EC 3.4.11.10
M28.002 (Metallo)
PF04389 (Peptidase_M28)
PF04151 (PPC)
[Graphical View]

KEGG enzyme name
bacterial leucyl aminopeptidase
Aeromonas proteolytica aminopeptidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q01693 AMPX_VIBPR Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Secreted. Binds 2 zinc ions per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00017 C00012 C00001 C00017 C00012 C00123
E.C.
Compound Zinc Protein Peptide H2O Protein Peptide L-Leucine
Type heavy metal peptide/protein peptide/protein H2O peptide/protein peptide/protein amino acids
ChEBI 29105
15377
15603
57427
PubChem 32051
22247451
962
6106
7045798
1ampA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Unbound Unbound
1cp6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Unbound Transition-state-analogue:BUB
1ft7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Analogue:PLU Unbound
1igbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Analogue:IPO Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;Q01693

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ampA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 151 HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1cp6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 151 HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1ft7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 151 HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1igbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 151 HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.396-397
[5]
Fig.7, p.4283-4285 4
[6]
p.9050-9053
[10]
Fig.10, p.7042-7045 4
[12]
p.1196-1199

References
[1]
Resource
Comments
Medline ID
PubMed ID 8357796
Journal Biochemistry
Year 1993
Volume 32
Pages 8465-78
Authors Kim H, Lipscomb WN
Title X-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.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-ray crystallography (1.8 Angstroms)
Medline ID 94373500
PubMed ID 8087555
Journal Structure
Year 1994
Volume 2
Pages 283-91
Authors Chevrier B, Schalk C, D'Orchymont H, Rondeau JM, Moras D, Tarnus C
Title Crystal structure of Aeromonas proteolytica aminopeptidase: a prototypical member of the co-catalytic zinc enzyme family.
Related PDB 1amp
Related UniProtKB Q01693
[3]
Resource
Comments
Medline ID
PubMed ID 7578088
Journal Biochemistry
Year 1995
Volume 34
Pages 14792-800
Authors Strater N, Lipscomb WN
Title Two-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.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography complex with inhibitor
Medline ID 96215434
PubMed ID 8647077
Journal Eur J Biochem
Year 1996
Volume 237
Pages 393-8
Authors Chevrier B, D'Orchymont H, Schalk C, Tarnus C, Moras D
Title The 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 PDB 1igb
Related UniProtKB Q01693
[5]
Resource
Comments mechanistic studies, catalysis
Medline ID
PubMed ID 9100023
Journal Biochemistry
Year 1997
Volume 36
Pages 4278-86
Authors Chen G, Edwards T, D'souza VM, Holz RC
Title Mechanistic studies on the aminopeptidase from Aeromonas proteolytica: a two-metal ion mechanism for peptide hydrolysis.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography (1.9 Angstroms)
Medline ID
PubMed ID 10413478
Journal Biochemistry
Year 1999
Volume 38
Pages 9048-53
Authors De Paola CC, Bennett B, Holz RC, Ringe D, Petsko GA
Title 1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development.
Related PDB 1cp6
Related UniProtKB
[7]
Resource
Comments inhibition, catalysis
Medline ID
PubMed ID 10471294
Journal Biochemistry
Year 1999
Volume 38
Pages 11433-9
Authors Ustynyuk L, Bennett B, Edwards T, Holz RC
Title Inhibition of the aminopeptidase from Aeromonas proteolytica by aliphatic alcohols. Characterization of the hydrophobic substrate recognition site.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10500145
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 11151-5
Authors Strater N, Sun L, Kantrowitz ER, Lipscomb WN
Title A bicarbonate ion as a general base in the mechanism of peptide hydrolysis by dizinc leucine aminopeptidase.
Related PDB
Related UniProtKB
[9]
Resource
Comments inhibition
Medline ID
PubMed ID 10569943
Journal Biochemistry
Year 1999
Volume 38
Pages 15587-96
Authors Huntington KM, Bienvenue DL, Wei Y, Bennett B, Holz RC, Pei D
Title Slow-binding inhibition of the aminopeptidase from Aeromonas proteolytica by peptide thiols: synthesis and spectroscopic characterization.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography (2.1 Angstroms)
Medline ID
PubMed ID 11401547
Journal Biochemistry
Year 2001
Volume 40
Pages 7035-46
Authors Stamper C, Bennett B, Edwards T, Holz RC, Ringe D, Petsko G
Title Inhibition of the aminopeptidase from Aeromonas proteolytica by L-leucinephosphonic acid. Spectroscopic and crystallographic characterization of the transition state of peptide hydrolysis.
Related PDB 1ft7
Related UniProtKB
[11]
Resource
Comments X-ray crystallography (1.53-1.80 Angstroms)
Medline ID
PubMed ID 11484227
Journal Proteins
Year 2001
Volume 44
Pages 490-504
Authors Gilboa R, Spungin-Bialik A, Wohlfahrt G, Schomburg D, Blumberg S, Shoham G
Title Interactions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11743734
Journal J Mol Biol
Year 2001
Volume 314
Pages 1191-207
Authors Wouters MA, Husain A
Title Changes in zinc ligation promote remodeling of the active site in the zinc hydrolase superfamily.
Related PDB
Related UniProtKB

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.

Created Updated
2002-09-27 2009-02-26