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P04825

- AMPN_ECOLI

UniProt

P04825 - AMPN_ECOLI

Protein

Aminopeptidase N

Gene

pepN

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 151 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    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

    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

    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10696. pepN.

    Subcellular locationi

    GO - Cellular componenti

    1. plasma membrane Source: UniProtKB-SubCell

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK01256.
    OMAiRWDAAQM.
    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

    MTQQPQAKYR HDYRAPDYQI TDIDLTFDLD AQKTVVTAVS QAVRHGASDA    50
    PLRLNGEDLK LVSVHINDEP WTAWKEEEGA LVISNLPERF TLKIINEISP 100
    AANTALEGLY QSGDALCTQC EAEGFRHITY YLDRPDVLAR FTTKIIADKI 150
    KYPFLLSNGN RVAQGELENG RHWVQWQDPF PKPCYLFALV AGDFDVLRDT 200
    FTTRSGREVA LELYVDRGNL DRAPWAMTSL KNSMKWDEER FGLEYDLDIY 250
    MIVAVDFFNM GAMENKGLNI FNSKYVLART DTATDKDYLD IERVIGHEYF 300
    HNWTGNRVTC RDWFQLSLKE GLTVFRDQEF SSDLGSRAVN RINNVRTMRG 350
    LQFAEDASPM AHPIRPDMVI EMNNFYTLTV YEKGAEVIRM IHTLLGEENF 400
    QKGMQLYFER HDGSAATCDD FVQAMEDASN VDLSHFRRWY SQSGTPIVTV 450
    KDDYNPETEQ YTLTISQRTP ATPDQAEKQP LHIPFAIELY DNEGKVIPLQ 500
    KGGHPVNSVL NVTQAEQTFV FDNVYFQPVP ALLCEFSAPV KLEYKWSDQQ 550
    LTFLMRHARN DFSRWDAAQS LLATYIKLNV ARHQQGQPLS LPVHVADAFR 600
    AVLLDEKIDP ALAAEILTLP SVNEMAELFD IIDPIAIAEV REALTRTLAT 650
    ELADELLAIY NANYQSEYRV EHEDIAKRTL RNACLRFLAF GETHLADVLV 700
    SKQFHEANNM TDALAALSAA VAAQLPCRDA LMQEYDDKWH QNGLVMDKWF 750
    ILQATSPAAN VLETVRGLLQ HRSFTMSNPN RIRSLIGAFA GSNPAAFHAE 800
    DGSGYLFLVE MLTDLNSRNP QVASRLIEPL IRLKRYDAKR QEKMRAALEQ 850
    LKGLENLSGD LYEKITKALA 870
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi C64833. DPECN.
    RefSeqi NP_415452.1. NC_000913.3.
    YP_489204.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2DQ6 X-ray 1.50 A 1-870 [» ]
    2DQM X-ray 1.60 A 1-870 [» ]
    2HPO X-ray 1.65 A 1-870 [» ]
    2HPT X-ray 2.30 A 1-870 [» ]
    2ZXG X-ray 1.55 A 1-870 [» ]
    3B2P X-ray 2.00 A 1-870 [» ]
    3B2X X-ray 1.50 A 1-870 [» ]
    3B34 X-ray 1.30 A 1-870 [» ]
    3B37 X-ray 1.70 A 1-870 [» ]
    3B3B X-ray 1.85 A 1-870 [» ]
    3KED X-ray 2.30 A 1-870 [» ]
    3PUU X-ray 2.15 A 1-870 [» ]
    3QJX X-ray 1.45 A 1-870 [» ]
    ProteinModelPortali P04825.
    SMRi P04825. Positions 5-870.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 851583. 1 interaction.
    DIPi DIP-10458N.
    IntActi P04825. 13 interactions.
    MINTi MINT-1310653.
    STRINGi 511145.b0932.

    Chemistry

    BindingDBi P04825.
    ChEMBLi CHEMBL4325.

    Protein family/group databases

    MEROPSi M01.005.

    Proteomic databases

    PaxDbi P04825.
    PRIDEi P04825.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74018 ; AAC74018 ; b0932 .
    BAA35684 ; BAA35684 ; BAA35684 .
    GeneIDi 12932886.
    947253.
    KEGGi ecj:Y75_p0904.
    eco:b0932.
    PATRICi 32117083. VBIEscCol129921_0966.

    Organism-specific databases

    EchoBASEi EB0690.
    EcoGenei EG10696. pepN.

    Phylogenomic databases

    eggNOGi COG0308.
    HOGENOMi HOG000257670.
    KOi K01256.
    OMAi RWDAAQM.
    OrthoDBi EOG693GJ0.
    PhylomeDBi P04825.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10696-MONOMER.
    ECOL316407:JW0915-MONOMER.
    MetaCyc:EG10696-MONOMER.
    RETL1328306-WGS:GSTH-1303-MONOMER.
    BRENDAi 3.4.11.2. 2026.

    Miscellaneous databases

    EvolutionaryTracei P04825.
    PROi P04825.

    Gene expression databases

    Genevestigatori P04825.

    Family and domain databases

    Gene3Di 1.25.50.10. 1 hit.
    InterProi IPR001930. Peptidase_M1.
    IPR014782. Peptidase_M1_N.
    IPR012779. Peptidase_M1_pepN.
    IPR024601. Peptidase_M1_pepN_C.
    [Graphical view ]
    PANTHERi PTHR11533. PTHR11533. 1 hit.
    Pfami PF11940. DUF3458. 1 hit.
    PF01433. Peptidase_M1. 1 hit.
    [Graphical view ]
    PRINTSi PR00756. ALADIPTASE.
    TIGRFAMsi TIGR02414. pepN_proteo. 1 hit.
    PROSITEi PS00142. ZINC_PROTEASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 151 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