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P09030

- EX3_ECOLI

UniProt

P09030 - EX3_ECOLI

Protein

Exodeoxyribonuclease III

Gene

xthA

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 154 (01 Oct 2014)
      Sequence version 4 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Major apurinic-apyrimidinic endonuclease of E.coli. It removes the damaged DNA at cytosines and guanines by cleaving on the 3'-side of the AP site by a beta-elimination reaction. It exhibits 3'-5'-exonuclease, 3'-phosphomonoesterase, 3'-repair diesterase and ribonuclease H activities.

    Catalytic activityi

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

    Cofactori

    Magnesium. Can also utilize manganese. Probably binds two magnesium or manganese ions per subunit By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi34 – 341Magnesium 1By similarity
    Active sitei109 – 1091By similarity
    Active sitei151 – 1511Proton donor/acceptorBy similarity
    Metal bindingi151 – 1511Magnesium 2By similarity
    Metal bindingi153 – 1531Magnesium 2By similarity
    Sitei153 – 1531Transition state stabilizerBy similarity
    Sitei229 – 2291Important for catalytic activityBy similarity
    Metal bindingi258 – 2581Magnesium 1By similarity
    Sitei259 – 2591Interaction with DNA substrateBy similarity

    GO - Molecular functioni

    1. DNA-(apurinic or apyrimidinic site) lyase activity Source: RefGenome
    2. DNA binding Source: InterPro
    3. double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: RefGenome
    4. exodeoxyribonuclease III activity Source: EcoCyc
    5. exonuclease activity Source: EcoCyc
    6. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. base-excision repair Source: RefGenome
    2. cellular response to DNA damage stimulus Source: EcoCyc
    3. DNA catabolic process, endonucleolytic Source: GOC
    4. DNA catabolic process, exonucleolytic Source: GOC
    5. nucleic acid phosphodiester bond hydrolysis Source: GOC

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11073-MONOMER.
    ECOL316407:JW1738-MONOMER.
    MetaCyc:EG11073-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exodeoxyribonuclease III (EC:3.1.11.2)
    Short name:
    EXO III
    Short name:
    Exonuclease III
    Alternative name(s):
    AP endonuclease VI
    Gene namesi
    Name:xthA
    Synonyms:xth
    Ordered Locus Names:b1749, JW1738
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11073. xthA.

    Subcellular locationi

    GO - Cellular componenti

    1. intracellular Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 268268Exodeoxyribonuclease IIIPRO_0000200021Add
    BLAST

    Proteomic databases

    PaxDbiP09030.
    PRIDEiP09030.

    2D gel databases

    SWISS-2DPAGEP09030.

    Expressioni

    Gene expression databases

    GenevestigatoriP09030.

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    DIPiDIP-11148N.
    IntActiP09030. 16 interactions.
    MINTiMINT-1243969.
    STRINGi511145.b1749.

    Structurei

    Secondary structure

    1
    268
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76
    Helixi11 – 133
    Helixi15 – 2511
    Beta strandi28 – 336
    Helixi39 – 413
    Helixi44 – 496
    Beta strandi53 – 597
    Beta strandi62 – 7110
    Beta strandi74 – 807
    Helixi85 – 884
    Beta strandi91 – 988
    Beta strandi101 – 1099
    Helixi121 – 13919
    Beta strandi146 – 1516
    Helixi158 – 1603
    Helixi165 – 17410
    Beta strandi176 – 1794
    Helixi181 – 19212
    Beta strandi195 – 1973
    Helixi198 – 2025
    Turni215 – 2184
    Helixi219 – 2224
    Beta strandi229 – 2346
    Helixi235 – 2384
    Beta strandi241 – 2466
    Helixi248 – 2514
    Beta strandi253 – 2553
    Beta strandi262 – 2665

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AKOX-ray1.70A1-268[»]
    ProteinModelPortaliP09030.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP09030.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DNA repair enzymes AP/ExoA family.Curated

    Phylogenomic databases

    eggNOGiCOG0708.
    HOGENOMiHOG000034587.
    KOiK01142.
    OMAiIEKPSDH.
    OrthoDBiEOG60SCPF.
    PhylomeDBiP09030.

    Family and domain databases

    Gene3Di3.60.10.10. 1 hit.
    InterProiIPR004808. AP_endonuc_1.
    IPR020847. AP_endonuclease_F1_BS.
    IPR020848. AP_endonuclease_F1_CS.
    IPR005135. Endo/exonuclease/phosphatase.
    [Graphical view]
    PANTHERiPTHR22748. PTHR22748. 1 hit.
    PfamiPF03372. Exo_endo_phos. 1 hit.
    [Graphical view]
    SUPFAMiSSF56219. SSF56219. 1 hit.
    TIGRFAMsiTIGR00633. xth. 1 hit.
    PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
    PS00727. AP_NUCLEASE_F1_2. 1 hit.
    PS00728. AP_NUCLEASE_F1_3. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P09030-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKFVSFNING LRARPHQLEA IVEKHQPDVI GLQETKVHDD MFPLEEVAKL    50
    GYNVFYHGQK GHYGVALLTK ETPIAVRRGF PGDDEEAQRR IIMAEIPSLL 100
    GNVTVINGYF PQGESRDHPI KFPAKAQFYQ NLQNYLETEL KRDNPVLIMG 150
    DMNISPTDLD IGIGEENRKR WLRTGKCSFL PEEREWMDRL MSWGLVDTFR 200
    HANPQTADRF SWFDYRSKGF DDNRGLRIDL LLASQPLAEC CVETGIDYEI 250
    RSMEKPSDHA PVWATFRR 268
    Length:268
    Mass (Da):30,969
    Last modified:November 1, 1997 - v4
    Checksum:i09E0E263DCF38634
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti49 – 502KL → NV in AAA24767. (PubMed:3049539)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X13002 Genomic DNA. Translation: CAA31424.1.
    M22592 Genomic DNA. Translation: AAA24767.1.
    U00096 Genomic DNA. Translation: AAC74819.1.
    AP009048 Genomic DNA. Translation: BAA15540.1.
    PIRiE64934. NCECX3.
    RefSeqiNP_416263.1. NC_000913.3.
    YP_490010.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74819; AAC74819; b1749.
    BAA15540; BAA15540; BAA15540.
    GeneIDi12932910.
    946254.
    KEGGiecj:Y75_p1724.
    eco:b1749.
    PATRICi32118809. VBIEscCol129921_1822.

    Cross-referencesi

    Web resourcesi

    Wikipedia

    Exonuclease III entry

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X13002 Genomic DNA. Translation: CAA31424.1 .
    M22592 Genomic DNA. Translation: AAA24767.1 .
    U00096 Genomic DNA. Translation: AAC74819.1 .
    AP009048 Genomic DNA. Translation: BAA15540.1 .
    PIRi E64934. NCECX3.
    RefSeqi NP_416263.1. NC_000913.3.
    YP_490010.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AKO X-ray 1.70 A 1-268 [» ]
    ProteinModelPortali P09030.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-11148N.
    IntActi P09030. 16 interactions.
    MINTi MINT-1243969.
    STRINGi 511145.b1749.

    2D gel databases

    SWISS-2DPAGE P09030.

    Proteomic databases

    PaxDbi P09030.
    PRIDEi P09030.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74819 ; AAC74819 ; b1749 .
    BAA15540 ; BAA15540 ; BAA15540 .
    GeneIDi 12932910.
    946254.
    KEGGi ecj:Y75_p1724.
    eco:b1749.
    PATRICi 32118809. VBIEscCol129921_1822.

    Organism-specific databases

    EchoBASEi EB1066.
    EcoGenei EG11073. xthA.

    Phylogenomic databases

    eggNOGi COG0708.
    HOGENOMi HOG000034587.
    KOi K01142.
    OMAi IEKPSDH.
    OrthoDBi EOG60SCPF.
    PhylomeDBi P09030.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11073-MONOMER.
    ECOL316407:JW1738-MONOMER.
    MetaCyc:EG11073-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P09030.
    PROi P09030.

    Gene expression databases

    Genevestigatori P09030.

    Family and domain databases

    Gene3Di 3.60.10.10. 1 hit.
    InterProi IPR004808. AP_endonuc_1.
    IPR020847. AP_endonuclease_F1_BS.
    IPR020848. AP_endonuclease_F1_CS.
    IPR005135. Endo/exonuclease/phosphatase.
    [Graphical view ]
    PANTHERi PTHR22748. PTHR22748. 1 hit.
    Pfami PF03372. Exo_endo_phos. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56219. SSF56219. 1 hit.
    TIGRFAMsi TIGR00633. xth. 1 hit.
    PROSITEi PS00726. AP_NUCLEASE_F1_1. 1 hit.
    PS00727. AP_NUCLEASE_F1_2. 1 hit.
    PS00728. AP_NUCLEASE_F1_3. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the xth gene of Escherichia coli K-12."
      Saporito S.M., Smith-White B.J., Cunningham R.P.
      J. Bacteriol. 170:4542-4547(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Wurst H., Hoheisel J.D., Pohl F.M.
      Submitted (NOV-1988) to the EMBL/GenBank/DDBJ databases
      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. "Cleavage of single- and double-stranded DNAs containing an abasic residue by Escherichia coli exonuclease III (AP endonuclease VI)."
      Shida T., Noda M., Sekiguchi J.
      Nucleic Acids Res. 24:4572-4576(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    7. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    8. "Structure and function of the multifunctional DNA-repair enzyme exonuclease III."
      Mol C.D., Kuo C.-F., Thayer M.M., Cunningham R.P., Tainer J.A.
      Nature 374:381-386(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), COFACTOR.

    Entry informationi

    Entry nameiEX3_ECOLI
    AccessioniPrimary (citable) accession number: P09030
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1988
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 154 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3