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P15288

- PEPD_ECOLI

UniProt

P15288 - PEPD_ECOLI

Protein

Cytosol non-specific dipeptidase

Gene

pepD

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 130 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Dipeptidase with broad substrate specificity. Requires dipeptide substrates with an unblocked N-terminus and the amino group in the alpha or beta position. Non-protein amino acids and proline are not accepted in the C-terminal position, whereas some dipeptide amides and formyl amino acids are hydrolyzed. Also shows cysteinylglycinase activity, which is sufficient for E.coli to utilize cysteinylglycine as a cysteine source.3 Publications

    Catalytic activityi

    Hydrolysis of dipeptides, preferentially hydrophobic dipeptides including prolyl amino acids.2 Publications

    Cofactori

    Binds 2 zinc ions per subunit. Can also use cobalt.1 Publication

    Enzyme regulationi

    Inhibited by metal chelators.1 Publication

    pH dependencei

    Optimum pH is 9.1 Publication

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi76 – 761Zinc 2By similarity
    Active sitei78 – 781By similarity
    Metal bindingi115 – 1151Zinc 1By similarity
    Metal bindingi115 – 1151Zinc 2By similarity
    Active sitei145 – 1451Proton acceptorBy similarity
    Metal bindingi146 – 1461Zinc 1By similarity
    Metal bindingi169 – 1691Zinc 2By similarity
    Metal bindingi457 – 4571Zinc 1By similarity

    GO - Molecular functioni

    1. dipeptidase activity Source: EcoCyc
    2. metallodipeptidase activity Source: EcoCyc
    3. zinc ion binding Source: EcoCyc

    GO - Biological processi

    1. peptide catabolic process Source: EcoliWiki

    Keywords - Molecular functioni

    Dipeptidase, Hydrolase, Metalloprotease, Protease

    Keywords - Ligandi

    Cobalt, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10695-MONOMER.
    ECOL316407:JW0227-MONOMER.
    MetaCyc:EG10695-MONOMER.

    Protein family/group databases

    MEROPSiM20.007.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytosol non-specific dipeptidase (EC:3.4.13.18)
    Alternative name(s):
    Aminoacyl-histidine dipeptidase
    Beta-alanyl-histidine dipeptidase
    Carnosinase
    Cysteinylglycinase
    Peptidase D
    Xaa-His dipeptidase
    Short name:
    X-His dipeptidase
    Gene namesi
    Name:pepD
    Synonyms:pepH
    Ordered Locus Names:b0237, JW0227
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10695. pepD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 485484Cytosol non-specific dipeptidasePRO_0000185354Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei296 – 2961N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    PaxDbiP15288.
    PRIDEiP15288.

    2D gel databases

    SWISS-2DPAGEP15288.

    Expressioni

    Gene expression databases

    GenevestigatoriP15288.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    hscBP0A6L91EBI-542419,EBI-561519
    yggXP0A8P31EBI-542419,EBI-1123057

    Protein-protein interaction databases

    DIPiDIP-10456N.
    IntActiP15288. 69 interactions.
    MINTiMINT-1252343.
    STRINGi511145.b0237.

    Structurei

    3D structure databases

    ProteinModelPortaliP15288.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase M20C family.Curated

    Phylogenomic databases

    eggNOGiCOG2195.
    HOGENOMiHOG000282306.
    KOiK01270.
    OMAiKGGYPGW.
    OrthoDBiEOG6BCSRT.
    PhylomeDBiP15288.

    Family and domain databases

    InterProiIPR002933. Peptidase_M20.
    IPR011650. Peptidase_M20_dimer.
    IPR001160. Peptidase_M20C.
    [Graphical view]
    PfamiPF07687. M20_dimer. 1 hit.
    PF01546. Peptidase_M20. 1 hit.
    [Graphical view]
    PIRSFiPIRSF016599. Xaa-His_dipept. 1 hit.
    PRINTSiPR00934. XHISDIPTASE.
    TIGRFAMsiTIGR01893. aa-his-dipept. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P15288-1 [UniParc]FASTAAdd to Basket

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    MSELSQLSPQ PLWDIFAKIC SIPHPSYHEE QLAEYIVGWA KEKGFHVERD    50
    QVGNILIRKP ATAGMENRKP VVLQAHLDMV PQKNNDTVHD FTKDPIQPYI 100
    DGEWVKARGT TLGADNGIGM ASALAVLADE NVVHGPLEVL LTMTEEAGMD 150
    GAFGLQGNWL QADILINTDS EEEGEIYMGC AGGIDFTSNL HLDREAVPAG 200
    FETFKLTLKG LKGGHSGGEI HVGLGNANKL LVRFLAGHAE ELDLRLIDFN 250
    GGTLRNAIPR EAFATIAVAA DKVDVLKSLV NTYQEILKNE LAEKEKNLAL 300
    LLDSVANDKA ALIAKSRDTF IRLLNATPNG VIRNSDVAKG VVETSLNVGV 350
    VTMTDNNVEI HCLIRSLIDS GKDYVVSMLD SLGKLAGAKT EAKGAYPGWQ 400
    PDANSPVMHL VRETYQRLFN KTPNIQIIHA GLECGLFKKP YPEMDMVSIG 450
    PTITGPHSPD EQVHIESVGH YWTLLTELLK EIPAK 485
    Length:485
    Mass (Da):52,915
    Last modified:January 23, 2007 - v3
    Checksum:iCD870032876460E1
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M34034 Unassigned DNA. Translation: AAA16111.1.
    U70214 Genomic DNA. Translation: AAB08657.1.
    U00096 Genomic DNA. Translation: AAC73341.1.
    AP009048 Genomic DNA. Translation: BAA77906.1.
    X14790 Genomic DNA. Translation: CAA32892.1.
    PIRiJU0300.
    RefSeqiNP_414772.1. NC_000913.3.
    YP_488532.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73341; AAC73341; b0237.
    BAA77906; BAA77906; BAA77906.
    GeneIDi12930771.
    945013.
    KEGGiecj:Y75_p0228.
    eco:b0237.
    PATRICi32115589. VBIEscCol129921_0239.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M34034 Unassigned DNA. Translation: AAA16111.1 .
    U70214 Genomic DNA. Translation: AAB08657.1 .
    U00096 Genomic DNA. Translation: AAC73341.1 .
    AP009048 Genomic DNA. Translation: BAA77906.1 .
    X14790 Genomic DNA. Translation: CAA32892.1 .
    PIRi JU0300.
    RefSeqi NP_414772.1. NC_000913.3.
    YP_488532.1. NC_007779.1.

    3D structure databases

    ProteinModelPortali P15288.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10456N.
    IntActi P15288. 69 interactions.
    MINTi MINT-1252343.
    STRINGi 511145.b0237.

    Protein family/group databases

    MEROPSi M20.007.

    2D gel databases

    SWISS-2DPAGE P15288.

    Proteomic databases

    PaxDbi P15288.
    PRIDEi P15288.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73341 ; AAC73341 ; b0237 .
    BAA77906 ; BAA77906 ; BAA77906 .
    GeneIDi 12930771.
    945013.
    KEGGi ecj:Y75_p0228.
    eco:b0237.
    PATRICi 32115589. VBIEscCol129921_0239.

    Organism-specific databases

    EchoBASEi EB0689.
    EcoGenei EG10695. pepD.

    Phylogenomic databases

    eggNOGi COG2195.
    HOGENOMi HOG000282306.
    KOi K01270.
    OMAi KGGYPGW.
    OrthoDBi EOG6BCSRT.
    PhylomeDBi P15288.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10695-MONOMER.
    ECOL316407:JW0227-MONOMER.
    MetaCyc:EG10695-MONOMER.

    Miscellaneous databases

    PROi P15288.

    Gene expression databases

    Genevestigatori P15288.

    Family and domain databases

    InterProi IPR002933. Peptidase_M20.
    IPR011650. Peptidase_M20_dimer.
    IPR001160. Peptidase_M20C.
    [Graphical view ]
    Pfami PF07687. M20_dimer. 1 hit.
    PF01546. Peptidase_M20. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF016599. Xaa-His_dipept. 1 hit.
    PRINTSi PR00934. XHISDIPTASE.
    TIGRFAMsi TIGR01893. aa-his-dipept. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Peptidase D gene (pepD) of Escherichia coli K-12: nucleotide sequence, transcript mapping, and comparison with other peptidase genes."
      Henrich B., Monnerjahn U., Plapp R.
      J. Bacteriol. 172:4641-4651(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: K12.
    2. "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region."
      Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.
      Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    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. "Accurate mapping of the Escherichia coli pepD gene by sequence analysis of its 5' flanking region."
      Henrich B., Schroeder U., Frank R.W., Plapp R.
      Mol. Gen. Genet. 215:369-373(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-56, PROTEIN SEQUENCE OF 2-13.
      Strain: K12.
    7. "Peptidase-deficient mutants of Escherichia coli."
      Miller C.G., Schwartz G.
      J. Bacteriol. 135:603-611(1978) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    8. "Peptidase D of Escherichia coli K-12, a metallopeptidase of low substrate specificity."
      Schroeder U., Henrich B., Fink J., Plapp R.
      FEMS Microbiol. Lett. 123:153-159(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    9. "Aminopeptidases A, B, and N and dipeptidase D are the four cysteinylglycinases of Escherichia coli K-12."
      Suzuki H., Kamatani S., Kim E.-S., Kumagai H.
      J. Bacteriol. 183:1489-1490(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
      Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
      Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-296, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiPEPD_ECOLI
    AccessioniPrimary (citable) accession number: P15288
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 130 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    External Data

    Dasty 3