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	Bound:2x_ZN	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
1cp6A	Bound:2x_ZN	Unbound	Unbound		Unbound	Unbound	Unbound	Transition-state-analogue:BUB
1ft7A	Bound:2x_ZN	Unbound	Unbound		Unbound	Unbound	Analogue:PLU	Unbound
1igbA	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	GLU 151	HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1cp6A	GLU 151	HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1ft7A	GLU 151	HIS 97;ASP 117;GLU 152;ASP 179;HIS 256(two Zn2+ binding)
1igbA	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.

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