Escherichia coli K-12 substr. MG1655 Enzyme: aminopeptidase N

Gene: pepN Accession Numbers: EG10696 (EcoCyc), b0932, ECK0923

Synonyms: α-aminoacylpeptide hydrolase

Regulation Summary Diagram: ?

Regulation summary diagram for pepN

Aminopeptidase N is an aminoendopeptidase, capable of breaking down small peptides as well as whole, native proteins [Lazdunski75, Chandu03].

Aminopeptidase N catalyzes the hydrolysis of a peptide bond either at the end of a small peptide or in the middle of a protein. In its exopeptidase activity, it shows a cleavage preference for basic and small amino acids, in the order arginine > alanine > lysine > glycine [Chandu03a]. Other substrates include cysteinylglycine [Suzuki01a]. Phosphorylation of peptide side chains near the cut site can prevent hydrolysis of the peptide bond [Fernandez96].

Some results suggest that aminopeptidase N synthesis is independent of growth conditions, though other experiments have demonstrated increased synthesis of this protein during phosphate starvation, anaerobiosis and growth on glycerol and succinate [McCaman82, Murgier82, Gharbi85].

Crystal structures of solitary aminopeptidase N and the enzyme complexed with bestatin have been determined to 1.5 and 1.6 Å resolution, respectively [Ito06].

Citations: [Latil76, Miller78]

Locations: inner membrane

Map Position: [989,845 -> 992,457] (21.33 centisomes, 77°)
Length: 2613 bp / 870 aa

Molecular Weight of Polypeptide: 98.919 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003171 , CGSC:414 , DIP:DIP-10458N , EchoBASE:EB0690 , EcoGene:EG10696 , EcoliWiki:b0932 , Mint:MINT-1310653 , ModBase:P04825 , OU-Microarray:b0932 , PortEco:pepN , Pride:P04825 , Protein Model Portal:P04825 , RefSeq:NP_415452 , RegulonDB:EG10696 , SMR:P04825 , String:511145.b0932 , UniProt:P04825

Relationship Links: InterPro:IN-FAMILY:IPR001930 , InterPro:IN-FAMILY:IPR012779 , InterPro:IN-FAMILY:IPR014782 , InterPro:IN-FAMILY:IPR024601 , Panther:IN-FAMILY:PTHR11533 , PDB:Structure:2DQ6 , PDB:Structure:2DQM , PDB:Structure:2HPO , PDB:Structure:2HPT , PDB:Structure:2ZXG , PDB:Structure:3B2P , PDB:Structure:3B2X , PDB:Structure:3B34 , PDB:Structure:3B37 , PDB:Structure:3B3B , PDB:Structure:3KED , PDB:Structure:3PUU , PDB:Structure:3QJX , Pfam:IN-FAMILY:PF01433 , Pfam:IN-FAMILY:PF11940 , Prints:IN-FAMILY:PR00756 , Prosite:IN-FAMILY:PS00142

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0043171 - peptide catabolic process Inferred from experiment [Miller78]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a, GOA01]
Molecular Function: GO:0004177 - aminopeptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Chandu03a]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0008237 - metallopeptidase activity Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: information transfer protein related turnover, degradation
metabolism degradation of macromolecules proteins/peptides/glycopeptides

Essentiality data for pepN knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Enzymatic reaction of: alanyl aminopeptidase (aminopeptidase N)

EC Number: 3.4.11.-

a polypeptide + H2O <=> 2 a polypeptide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Enzymatic reaction of: alanyl aminopeptidase (aminopeptidase N)

EC Number:

a polypeptide + H2O <=> a polypeptide + an L-amino acid

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Enzymatic reaction of: cysteinylglycine dipeptidase (aminopeptidase N)

L-cysteinyl-glycine + H2O <=> L-cysteine + glycine

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of aminopeptidase N with features indicated

Feature Class Location Common Name Citations Comment
Cleavage-of-Initial-Methionine 1  
[Bally86, UniProt11]
UniProt: Removed.
Chain 2 -> 870  
UniProt: Aminopeptidase N;
Sequence-Conflict 76  
[Bally86, UniProt10a]
UniProt: (in Ref. 7; CAA27647);
Amino-Acid-Sites-That-Bind 121  
UniProt: Substrate.
Protein-Segment 261 -> 265  
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Metal-Binding-Site 297  
UniProt: Zinc; catalytic.
Metal-Binding-Site 297, 298, 301, 320 Metal-Binding-Site
This metal-binding motif was identified in a crystal structure [Ito06].
Active-Site 298  
[FournieZaluski09, Addlagatta08, Ito06, UniProt15]
UniProt: Proton acceptor.
Metal-Binding-Site 301  
UniProt: Zinc; catalytic.
Metal-Binding-Site 320  
UniProt: Zinc; catalytic.
Active-Site 381  
UniProt: Proton donor; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0932 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10696; confirmed by SwissProt match.


Addlagatta08: Addlagatta A, Gay L, Matthews BW (2008). "Structural basis for the unusual specificity of Escherichia coli aminopeptidase N." Biochemistry 47(19);5303-11. PMID: 18416562

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bally86: Bally M, Foglino M, Bruschi M, Murgier M, Lazdunski A (1986). "Nucleotide sequence of the promoter and amino-terminal encoding region of the Escherichia coli pepN gene." Eur J Biochem 155(3);565-9. PMID: 2869947

Chandu03: Chandu D, Kumar A, Nandi D (2003). "PepN, the major Suc-LLVY-AMC-hydrolyzing enzyme in Escherichia coli, displays functional similarity with downstream processing enzymes in Archaea and eukarya. Implications in cytosolic protein degradation." J Biol Chem 278(8);5548-56. PMID: 12482750

Chandu03a: Chandu D, Nandi D (2003). "PepN is the major aminopeptidase in Escherichia coli: insights on substrate specificity and role during sodium-salicylate-induced stress." Microbiology 149(12): 3437-47. PMID: 14663077

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Fernandez96: Fernandez Murray P, Hammerschmidt P, Samela A, Passeron S (1996). "Peptide degradation: effect of substrate phosphorylation on aminopeptidasic hydrolysis." Int J Biochem Cell Biol 28(4);451-6. PMID: 9026356

FournieZaluski09: Fournie-Zaluski MC, Poras H, Roques BP, Nakajima Y, Ito K, Yoshimoto T (2009). "Structure of aminopeptidase N from Escherichia coli complexed with the transition-state analogue aminophosphinic inhibitor PL250." Acta Crystallogr D Biol Crystallogr 65(Pt 8);814-22. PMID: 19622865

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gharbi85: Gharbi S, Belaich A, Murgier M, Lazdunski A (1985). "Multiple controls exerted on in vivo expression of the pepN gene in Escherichia coli: studies with pepN-lacZ operon and protein fusion strains." J Bacteriol 163(3);1191-5. PMID: 2863254

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Ito06: Ito K, Nakajima Y, Onohara Y, Takeo M, Nakashima K, Matsubara F, Ito T, Yoshimoto T (2006). "Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognition." J Biol Chem 281(44);33664-76. PMID: 16885166

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Latil76: Latil M, Murgier M, Lazdunski A, Lazdunski C (1976). "Isolation and genetic mapping of Escherichia coli aminopeptidase mutants." Mol Gen Genet 148(1);43-7. PMID: 792681

Lazdunski75: Lazdunski C, Busuttil J, Lazdunski A (1975). "Purification and properties of a periplasmic aminoendopeptidase from Escherichia coli." Eur J Biochem 60(2);363-9. PMID: 1271

McCaman82: McCaman MT, McPartland A, Villarejo MR (1982). "Genetics and regulation of peptidase N in Escherichia coli K-12." J Bacteriol 152(2);848-54. PMID: 6752120

Miller78: Miller CG, Schwartz G (1978). "Peptidase-deficient mutants of Escherichia coli." J Bacteriol 135(2);603-11. PMID: 355237

Murgier82: Murgier M, Gharbi S (1982). "Fusion of the lac genes to the promoter for the aminopeptidase N gene of Escherichia coli." Mol Gen Genet 187(2);316-9. PMID: 6129564

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Suzuki01a: Suzuki H, Kamatani S, Kim ES, Kumagai H (2001). "Aminopeptidases A, B, and N and dipeptidase D are the four cysteinylglycinases of Escherichia coli K-12." J Bacteriol 183(4);1489-90. PMID: 11157967

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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