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Protein

Aminopeptidase N

Gene

pepN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.

Catalytic activityi

Release of an N-terminal amino acid, Xaa-|-Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide.3 Publications

Cofactori

Zn2+3 PublicationsNote: Binds 1 zinc ion per subunit.3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei121 – 1211Substrate
Metal bindingi297 – 2971Zinc; catalytic
Active sitei298 – 2981Proton acceptor3 Publications
Metal bindingi301 – 3011Zinc; catalytic
Metal bindingi320 – 3201Zinc; catalytic
Sitei381 – 3811Transition state stabilizerCurated

GO - Molecular functioni

  1. aminopeptidase activity Source: EcoliWiki
  2. identical protein binding Source: IntAct
  3. metallopeptidase activity Source: UniProtKB-KW
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. peptide catabolic process Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Aminopeptidase, Hydrolase, Metalloprotease, Protease

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10696-MONOMER.
ECOL316407:JW0915-MONOMER.
MetaCyc:EG10696-MONOMER.
RETL1328306-WGS:GSTH-1303-MONOMER.
BRENDAi3.4.11.2. 2026.

Protein family/group databases

MEROPSiM01.005.

Names & Taxonomyi

Protein namesi
Recommended name:
Aminopeptidase N (EC:3.4.11.2)
Alternative name(s):
Alpha-aminoacylpeptide hydrolase
Gene namesi
Name:pepN
Ordered Locus Names:b0932, JW0915
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10696. pepN.

Subcellular locationi

GO - Cellular componenti

  1. plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 870869Aminopeptidase NPRO_0000095069Add
BLAST

Proteomic databases

PaxDbiP04825.
PRIDEiP04825.

Expressioni

Gene expression databases

GenevestigatoriP04825.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-545385,EBI-545385

Protein-protein interaction databases

BioGridi851583. 1 interaction.
DIPiDIP-10458N.
IntActiP04825. 13 interactions.
MINTiMINT-1310653.
STRINGi511145.b0932.

Structurei

Secondary structure

1
870
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 123Combined sources
Beta strandi17 – 2812Combined sources
Beta strandi34 – 4411Combined sources
Beta strandi52 – 554Combined sources
Beta strandi60 – 667Combined sources
Beta strandi73 – 775Combined sources
Beta strandi80 – 834Combined sources
Beta strandi88 – 9811Combined sources
Helixi100 – 1023Combined sources
Beta strandi108 – 1125Combined sources
Beta strandi115 – 1195Combined sources
Turni121 – 1244Combined sources
Helixi125 – 1273Combined sources
Beta strandi129 – 1313Combined sources
Beta strandi139 – 14810Combined sources
Turni149 – 1513Combined sources
Beta strandi154 – 16613Combined sources
Beta strandi171 – 18212Combined sources
Helixi184 – 1863Combined sources
Beta strandi189 – 1924Combined sources
Beta strandi195 – 2028Combined sources
Beta strandi208 – 2158Combined sources
Helixi220 – 2223Combined sources
Helixi224 – 24118Combined sources
Beta strandi247 – 25610Combined sources
Beta strandi259 – 2635Combined sources
Beta strandi268 – 2725Combined sources
Helixi273 – 2753Combined sources
Turni280 – 2823Combined sources
Helixi285 – 30016Combined sources
Turni301 – 3033Combined sources
Turni305 – 3073Combined sources
Beta strandi308 – 3125Combined sources
Helixi313 – 3153Combined sources
Helixi316 – 33419Combined sources
Helixi337 – 35014Combined sources
Helixi352 – 3565Combined sources
Beta strandi367 – 3704Combined sources
Helixi372 – 3754Combined sources
Helixi378 – 41134Combined sources
Beta strandi414 – 4163Combined sources
Helixi418 – 42912Combined sources
Turni434 – 4374Combined sources
Helixi438 – 4414Combined sources
Beta strandi447 – 4559Combined sources
Turni456 – 4594Combined sources
Beta strandi460 – 4689Combined sources
Beta strandi483 – 4908Combined sources
Beta strandi508 – 5125Combined sources
Beta strandi514 – 5218Combined sources
Beta strandi529 – 5335Combined sources
Helixi534 – 5363Combined sources
Beta strandi541 – 5433Combined sources
Helixi548 – 55710Combined sources
Helixi561 – 58424Combined sources
Helixi593 – 60412Combined sources
Beta strandi606 – 6083Combined sources
Helixi610 – 6167Combined sources
Helixi622 – 6265Combined sources
Helixi634 – 65118Combined sources
Helixi653 – 66210Combined sources
Helixi672 – 68918Combined sources
Helixi693 – 70614Combined sources
Helixi710 – 72213Combined sources
Helixi728 – 73912Combined sources
Helixi743 – 75412Combined sources
Helixi761 – 7688Combined sources
Helixi779 – 79214Combined sources
Helixi794 – 7974Combined sources
Helixi803 – 81816Combined sources
Helixi820 – 83112Combined sources
Helixi832 – 8354Combined sources
Helixi838 – 85215Combined sources
Helixi859 – 86911Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DQ6X-ray1.50A1-870[»]
2DQMX-ray1.60A1-870[»]
2HPOX-ray1.65A1-870[»]
2HPTX-ray2.30A1-870[»]
2ZXGX-ray1.55A1-870[»]
3B2PX-ray2.00A1-870[»]
3B2XX-ray1.50A1-870[»]
3B34X-ray1.30A1-870[»]
3B37X-ray1.70A1-870[»]
3B3BX-ray1.85A1-870[»]
3KEDX-ray2.30A1-870[»]
3PUUX-ray2.15A1-870[»]
3QJXX-ray1.45A1-870[»]
ProteinModelPortaliP04825.
SMRiP04825. Positions 5-870.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04825.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni261 – 2655Substrate binding

Sequence similaritiesi

Belongs to the peptidase M1 family.Curated

Phylogenomic databases

eggNOGiCOG0308.
HOGENOMiHOG000257670.
InParanoidiP04825.
KOiK01256.
OMAiMIVAVND.
OrthoDBiEOG693GJ0.
PhylomeDBiP04825.

Family and domain databases

Gene3Di1.25.50.10. 1 hit.
InterProiIPR001930. Peptidase_M1.
IPR014782. Peptidase_M1_N.
IPR012779. Peptidase_M1_pepN.
IPR024601. Peptidase_M1_pepN_C.
[Graphical view]
PANTHERiPTHR11533. PTHR11533. 1 hit.
PfamiPF11940. DUF3458. 1 hit.
PF01433. Peptidase_M1. 1 hit.
[Graphical view]
PRINTSiPR00756. ALADIPTASE.
TIGRFAMsiTIGR02414. pepN_proteo. 1 hit.
PROSITEiPS00142. ZINC_PROTEASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04825-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQQPQAKYR HDYRAPDYQI TDIDLTFDLD AQKTVVTAVS QAVRHGASDA
60 70 80 90 100
PLRLNGEDLK LVSVHINDEP WTAWKEEEGA LVISNLPERF TLKIINEISP
110 120 130 140 150
AANTALEGLY QSGDALCTQC EAEGFRHITY YLDRPDVLAR FTTKIIADKI
160 170 180 190 200
KYPFLLSNGN RVAQGELENG RHWVQWQDPF PKPCYLFALV AGDFDVLRDT
210 220 230 240 250
FTTRSGREVA LELYVDRGNL DRAPWAMTSL KNSMKWDEER FGLEYDLDIY
260 270 280 290 300
MIVAVDFFNM GAMENKGLNI FNSKYVLART DTATDKDYLD IERVIGHEYF
310 320 330 340 350
HNWTGNRVTC RDWFQLSLKE GLTVFRDQEF SSDLGSRAVN RINNVRTMRG
360 370 380 390 400
LQFAEDASPM AHPIRPDMVI EMNNFYTLTV YEKGAEVIRM IHTLLGEENF
410 420 430 440 450
QKGMQLYFER HDGSAATCDD FVQAMEDASN VDLSHFRRWY SQSGTPIVTV
460 470 480 490 500
KDDYNPETEQ YTLTISQRTP ATPDQAEKQP LHIPFAIELY DNEGKVIPLQ
510 520 530 540 550
KGGHPVNSVL NVTQAEQTFV FDNVYFQPVP ALLCEFSAPV KLEYKWSDQQ
560 570 580 590 600
LTFLMRHARN DFSRWDAAQS LLATYIKLNV ARHQQGQPLS LPVHVADAFR
610 620 630 640 650
AVLLDEKIDP ALAAEILTLP SVNEMAELFD IIDPIAIAEV REALTRTLAT
660 670 680 690 700
ELADELLAIY NANYQSEYRV EHEDIAKRTL RNACLRFLAF GETHLADVLV
710 720 730 740 750
SKQFHEANNM TDALAALSAA VAAQLPCRDA LMQEYDDKWH QNGLVMDKWF
760 770 780 790 800
ILQATSPAAN VLETVRGLLQ HRSFTMSNPN RIRSLIGAFA GSNPAAFHAE
810 820 830 840 850
DGSGYLFLVE MLTDLNSRNP QVASRLIEPL IRLKRYDAKR QEKMRAALEQ
860 870
LKGLENLSGD LYEKITKALA
Length:870
Mass (Da):98,919
Last modified:January 23, 2007 - v2
Checksum:i7C18C6BD8F2E5131
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti76 – 761E → D in CAA27647 (PubMed:2869947).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04020 Genomic DNA. Translation: CAA27647.1.
X03709 Genomic DNA. Translation: CAA27336.1.
M15676 Genomic DNA. Translation: AAA24318.1.
U00096 Genomic DNA. Translation: AAC74018.1.
AP009048 Genomic DNA. Translation: BAA35684.1.
M15273 Genomic DNA. Translation: AAA24317.1.
PIRiC64833. DPECN.
RefSeqiNP_415452.1. NC_000913.3.
YP_489204.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74018; AAC74018; b0932.
BAA35684; BAA35684; BAA35684.
GeneIDi12932886.
947253.
KEGGiecj:Y75_p0904.
eco:b0932.
PATRICi32117083. VBIEscCol129921_0966.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04020 Genomic DNA. Translation: CAA27647.1.
X03709 Genomic DNA. Translation: CAA27336.1.
M15676 Genomic DNA. Translation: AAA24318.1.
U00096 Genomic DNA. Translation: AAC74018.1.
AP009048 Genomic DNA. Translation: BAA35684.1.
M15273 Genomic DNA. Translation: AAA24317.1.
PIRiC64833. DPECN.
RefSeqiNP_415452.1. NC_000913.3.
YP_489204.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DQ6X-ray1.50A1-870[»]
2DQMX-ray1.60A1-870[»]
2HPOX-ray1.65A1-870[»]
2HPTX-ray2.30A1-870[»]
2ZXGX-ray1.55A1-870[»]
3B2PX-ray2.00A1-870[»]
3B2XX-ray1.50A1-870[»]
3B34X-ray1.30A1-870[»]
3B37X-ray1.70A1-870[»]
3B3BX-ray1.85A1-870[»]
3KEDX-ray2.30A1-870[»]
3PUUX-ray2.15A1-870[»]
3QJXX-ray1.45A1-870[»]
ProteinModelPortaliP04825.
SMRiP04825. Positions 5-870.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi851583. 1 interaction.
DIPiDIP-10458N.
IntActiP04825. 13 interactions.
MINTiMINT-1310653.
STRINGi511145.b0932.

Chemistry

BindingDBiP04825.
ChEMBLiCHEMBL4325.

Protein family/group databases

MEROPSiM01.005.

Proteomic databases

PaxDbiP04825.
PRIDEiP04825.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74018; AAC74018; b0932.
BAA35684; BAA35684; BAA35684.
GeneIDi12932886.
947253.
KEGGiecj:Y75_p0904.
eco:b0932.
PATRICi32117083. VBIEscCol129921_0966.

Organism-specific databases

EchoBASEiEB0690.
EcoGeneiEG10696. pepN.

Phylogenomic databases

eggNOGiCOG0308.
HOGENOMiHOG000257670.
InParanoidiP04825.
KOiK01256.
OMAiMIVAVND.
OrthoDBiEOG693GJ0.
PhylomeDBiP04825.

Enzyme and pathway databases

BioCyciEcoCyc:EG10696-MONOMER.
ECOL316407:JW0915-MONOMER.
MetaCyc:EG10696-MONOMER.
RETL1328306-WGS:GSTH-1303-MONOMER.
BRENDAi3.4.11.2. 2026.

Miscellaneous databases

EvolutionaryTraceiP04825.
PROiP04825.

Gene expression databases

GenevestigatoriP04825.

Family and domain databases

Gene3Di1.25.50.10. 1 hit.
InterProiIPR001930. Peptidase_M1.
IPR014782. Peptidase_M1_N.
IPR012779. Peptidase_M1_pepN.
IPR024601. Peptidase_M1_pepN_C.
[Graphical view]
PANTHERiPTHR11533. PTHR11533. 1 hit.
PfamiPF11940. DUF3458. 1 hit.
PF01433. Peptidase_M1. 1 hit.
[Graphical view]
PRINTSiPR00756. ALADIPTASE.
TIGRFAMsiTIGR02414. pepN_proteo. 1 hit.
PROSITEiPS00142. ZINC_PROTEASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the pepN gene encoding aminopeptidase N of Escherichia coli."
    Foglino M., Gharbi S., Lazdunski A.
    Gene 49:303-309(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The nucleotide sequence of the pepN gene and its over-expression in Escherichia coli."
    McCaman M.T., Gabe J.D.
    Gene 48:145-153(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Sequence of the promoter and 5' coding region of pepN, and the amino-terminus of peptidase N from Escherichia coli K-12."
    McCaman M.T., Gabe J.D.
    Mol. Gen. Genet. 204:148-152(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-242.
    Strain: K12.
  7. "Nucleotide sequence of the promoter and amino-terminal encoding region of the Escherichia coli pepN gene."
    Bally M., Foglino M., Bruschi M., Murgier M., Lazdunski A.
    Eur. J. Biochem. 155:565-569(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-177, PROTEIN SEQUENCE OF 2-22.
  8. "Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognition."
    Ito K., Nakajima Y., Onohara Y., Takeo M., Nakashima K., Matsubara F., Ito T., Yoshimoto T.
    J. Biol. Chem. 281:33664-33676(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH ZINC IONS AND BESTATIN, ACTIVE SITE, COFACTOR, CATALYTIC ACTIVITY.
  9. "Structural basis for the unusual specificity of Escherichia coli aminopeptidase N."
    Addlagatta A., Gay L., Matthews B.W.
    Biochemistry 47:5303-5311(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) IN COMPLEXES WITH ZINC IONS AND SUBSTRATE ANALOGS, CATALYTIC ACTIVITY, ACTIVE SITE, COFACTOR.
  10. "Structure of aminopeptidase N from Escherichia coli complexed with the transition-state analogue aminophosphinic inhibitor PL250."
    Fournie-Zaluski M.C., Poras H., Roques B.P., Nakajima Y., Ito K., Yoshimoto T.
    Acta Crystallogr. D 65:814-822(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH ZINC IONS AND TRANSITION-STATE ANALOG PL250, ACTIVE SITE, COFACTOR, CATALYTIC ACTIVITY.

Entry informationi

Entry nameiAMPN_ECOLI
AccessioniPrimary (citable) accession number: P04825
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: January 7, 2015
This is version 154 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.