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P04995

- EX1_ECOLI

UniProt

P04995 - EX1_ECOLI

Protein

Exodeoxyribonuclease I

Gene

sbcB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 141 (01 Oct 2014)
      Sequence version 2 (01 Feb 1994)
      Previous versions | rss
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    Functioni

    Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease AP lyase.1 Publication

    Catalytic activityi

    Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.

    GO - Molecular functioni

    1. exodeoxyribonuclease I activity Source: EcoCyc
    2. nucleic acid binding Source: InterPro

    GO - Biological processi

    1. DNA catabolic process Source: EcoCyc
    2. DNA catabolic process, exonucleolytic Source: GOC
    3. DNA repair Source: UniProtKB-KW

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    DNA damage, DNA repair

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10926-MONOMER.
    ECOL316407:JW1993-MONOMER.
    MetaCyc:EG10926-MONOMER.
    BRENDAi3.1.11.1. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exodeoxyribonuclease I (EC:3.1.11.1)
    Short name:
    Exonuclease I
    Alternative name(s):
    DNA deoxyribophosphodiesterase
    Short name:
    dRPase
    Gene namesi
    Name:sbcB
    Synonyms:cpeA, xonA
    Ordered Locus Names:b2011, JW1993
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10926. sbcB.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 475475Exodeoxyribonuclease IPRO_0000087110Add
    BLAST

    Proteomic databases

    PaxDbiP04995.
    PRIDEiP04995.

    Expressioni

    Gene expression databases

    GenevestigatoriP04995.

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-10827N.
    IntActiP04995. 6 interactions.
    MINTiMINT-1241098.
    STRINGi511145.b2011.

    Structurei

    Secondary structure

    1
    475
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 2112
    Turni23 – 253
    Beta strandi28 – 369
    Beta strandi47 – 515
    Helixi61 – 677
    Helixi71 – 777
    Helixi81 – 9212
    Beta strandi97 – 1037
    Turni104 – 1074
    Helixi108 – 11811
    Helixi125 – 1273
    Helixi129 – 1313
    Beta strandi133 – 1364
    Helixi137 – 14711
    Beta strandi160 – 1623
    Helixi166 – 1727
    Helixi185 – 20016
    Helixi202 – 2109
    Helixi214 – 2196
    Turni223 – 2264
    Beta strandi229 – 2324
    Helixi234 – 2363
    Helixi238 – 2403
    Beta strandi243 – 2519
    Beta strandi258 – 2636
    Helixi269 – 2735
    Helixi276 – 28510
    Helixi287 – 2893
    Beta strandi298 – 3025
    Helixi303 – 3053
    Beta strandi308 – 3114
    Helixi312 – 3143
    Helixi317 – 3237
    Helixi327 – 33913
    Helixi343 – 3464
    Helixi363 – 3653
    Helixi367 – 3693
    Helixi374 – 38512
    Turni388 – 3903
    Turni391 – 3933
    Helixi402 – 41413
    Helixi416 – 4183
    Helixi421 – 43414
    Helixi437 – 45317
    Turni454 – 4563
    Helixi458 – 47316

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FXXX-ray2.40A1-475[»]
    2QXFX-ray1.50A1-475[»]
    3C94X-ray2.70A1-475[»]
    3C95X-ray1.70A1-475[»]
    3HL8X-ray1.55A1-475[»]
    3HP9X-ray1.60A1-475[»]
    4HCBX-ray2.00A/B1-475[»]
    4HCCX-ray2.96A/B1-475[»]
    4JRPX-ray1.95A/B1-475[»]
    4JRQX-ray3.00A/B1-475[»]
    4JS4X-ray3.10A/B1-475[»]
    4JS5X-ray3.50A/B1-475[»]
    ProteinModelPortaliP04995.
    SMRiP04995. Positions 8-475.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04995.

    Family & Domainsi

    Phylogenomic databases

    eggNOGiCOG2925.
    HOGENOMiHOG000276591.
    KOiK01141.
    OMAiNFFDPYA.
    OrthoDBiEOG6MWN7F.
    PhylomeDBiP04995.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    InterProiIPR023607. Exodeoxyribonuclease_I.
    IPR013620. Exonuc_X-T_C.
    IPR013520. Exonuclease_RNaseT/DNA_pol3.
    IPR012337. RNaseH-like_dom.
    [Graphical view]
    PfamiPF08411. Exonuc_X-T_C. 1 hit.
    PF00929. RNase_T. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000977. Exodeoxyribonuclease_I. 1 hit.
    SUPFAMiSSF53098. SSF53098. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P04995-1 [UniParc]FASTAAdd to Basket

    « Hide

    MMNDGKQQST FLFHDYETFG THPALDRPAQ FAAIRTDSEF NVIGEPEVFY    50
    CKPADDYLPQ PGAVLITGIT PQEARAKGEN EAAFAARIHS LFTVPKTCIL 100
    GYNNVRFDDE VTRNIFYRNF YDPYAWSWQH DNSRWDLLDV MRACYALRPE 150
    GINWPENDDG LPSFRLEHLT KANGIEHSNA HDAMADVYAT IAMAKLVKTR 200
    QPRLFDYLFT HRNKHKLMAL IDVPQMKPLV HVSGMFGAWR GNTSWVAPLA 250
    WHPENRNAVI MVDLAGDISP LLELDSDTLR ERLYTAKTDL GDNAAVPVKL 300
    VHINKCPVLA QANTLRPEDA DRLGINRQHC LDNLKILREN PQVREKVVAI 350
    FAEAEPFTPS DNVDAQLYNG FFSDADRAAM KIVLETEPRN LPALDITFVD 400
    KRIEKLLFNY RARNFPGTLD YAEQQRWLEH RRQVFTPEFL QGYADELQML 450
    VQQYADDKEK VALLKALWQY AEEIV 475
    Length:475
    Mass (Da):54,501
    Last modified:February 1, 1994 - v2
    Checksum:iA6A02AC17922C313
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti210 – 2189Missing in AAA19938. (PubMed:3539937)Curated
    Sequence conflicti225 – 2251Q → H in AAA19938. (PubMed:3539937)Curated
    Sequence conflicti343 – 3431V → E in AAA19938. (PubMed:3539937)Curated
    Sequence conflicti475 – 4751V → A in AAA19938. (PubMed:3539937)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02641 Unassigned DNA. Translation: AAA19938.1.
    U00009 Genomic DNA. Translation: AAA16417.1.
    U00096 Genomic DNA. Translation: AAC75072.1.
    AP009048 Genomic DNA. Translation: BAA15839.1.
    PIRiB64966. NCECX1.
    RefSeqiNP_416515.1. NC_000913.3.
    YP_490253.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75072; AAC75072; b2011.
    BAA15839; BAA15839; BAA15839.
    GeneIDi12931420.
    946529.
    KEGGiecj:Y75_p1973.
    eco:b2011.
    PATRICi32119357. VBIEscCol129921_2088.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02641 Unassigned DNA. Translation: AAA19938.1 .
    U00009 Genomic DNA. Translation: AAA16417.1 .
    U00096 Genomic DNA. Translation: AAC75072.1 .
    AP009048 Genomic DNA. Translation: BAA15839.1 .
    PIRi B64966. NCECX1.
    RefSeqi NP_416515.1. NC_000913.3.
    YP_490253.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1FXX X-ray 2.40 A 1-475 [» ]
    2QXF X-ray 1.50 A 1-475 [» ]
    3C94 X-ray 2.70 A 1-475 [» ]
    3C95 X-ray 1.70 A 1-475 [» ]
    3HL8 X-ray 1.55 A 1-475 [» ]
    3HP9 X-ray 1.60 A 1-475 [» ]
    4HCB X-ray 2.00 A/B 1-475 [» ]
    4HCC X-ray 2.96 A/B 1-475 [» ]
    4JRP X-ray 1.95 A/B 1-475 [» ]
    4JRQ X-ray 3.00 A/B 1-475 [» ]
    4JS4 X-ray 3.10 A/B 1-475 [» ]
    4JS5 X-ray 3.50 A/B 1-475 [» ]
    ProteinModelPortali P04995.
    SMRi P04995. Positions 8-475.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10827N.
    IntActi P04995. 6 interactions.
    MINTi MINT-1241098.
    STRINGi 511145.b2011.

    Proteomic databases

    PaxDbi P04995.
    PRIDEi P04995.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75072 ; AAC75072 ; b2011 .
    BAA15839 ; BAA15839 ; BAA15839 .
    GeneIDi 12931420.
    946529.
    KEGGi ecj:Y75_p1973.
    eco:b2011.
    PATRICi 32119357. VBIEscCol129921_2088.

    Organism-specific databases

    EchoBASEi EB0919.
    EcoGenei EG10926. sbcB.

    Phylogenomic databases

    eggNOGi COG2925.
    HOGENOMi HOG000276591.
    KOi K01141.
    OMAi NFFDPYA.
    OrthoDBi EOG6MWN7F.
    PhylomeDBi P04995.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10926-MONOMER.
    ECOL316407:JW1993-MONOMER.
    MetaCyc:EG10926-MONOMER.
    BRENDAi 3.1.11.1. 2026.

    Miscellaneous databases

    EvolutionaryTracei P04995.
    PROi P04995.

    Gene expression databases

    Genevestigatori P04995.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    InterProi IPR023607. Exodeoxyribonuclease_I.
    IPR013620. Exonuc_X-T_C.
    IPR013520. Exonuclease_RNaseT/DNA_pol3.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF08411. Exonuc_X-T_C. 1 hit.
    PF00929. RNase_T. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000977. Exodeoxyribonuclease_I. 1 hit.
    SUPFAMi SSF53098. SSF53098. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Determination of the nucleotide sequence for the exonuclease I structural gene (sbcB) of Escherichia coli K12."
      Phillips G.J., Kushner S.R.
      J. Biol. Chem. 262:455-459(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-12.
      Strain: K12.
    2. "Automated multiplex sequencing of the E.coli genome."
      Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
      Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / BHB2600.
    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. "DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I."
      Sandigursky M., Franklin W.A.
      Nucleic Acids Res. 20:4699-4703(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A DRPASE.

    Entry informationi

    Entry nameiEX1_ECOLI
    AccessioniPrimary (citable) accession number: P04995
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: February 1, 1994
    Last modified: October 1, 2014
    This is version 141 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

    External Data

    Dasty 3