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P0AB83

- END3_ECOLI

UniProt

P0AB83 - END3_ECOLI

Protein

Endonuclease III

Gene

nth

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 90 (01 Oct 2014)
      Sequence version 1 (08 Nov 2005)
      Previous versions | rss
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    Functioni

    DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.3 PublicationsUniRule annotation

    Catalytic activityi

    The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.1 PublicationUniRule annotation

    Cofactori

    Binds 1 4Fe-4S cluster. The cluster does not appear to play a role in catalysis, but is probably involved in DNA-binding and proper positioning of the enzyme along the DNA strand.2 PublicationsUniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi187 – 1871Iron-sulfur (4Fe-4S)
    Metal bindingi194 – 1941Iron-sulfur (4Fe-4S)
    Metal bindingi197 – 1971Iron-sulfur (4Fe-4S)
    Metal bindingi203 – 2031Iron-sulfur (4Fe-4S)

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
    2. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-HAMAP
    3. DNA binding Source: UniProtKB-HAMAP
    4. DNA N-glycosylase activity Source: UniProtKB-HAMAP
    5. metal ion binding Source: UniProtKB-KW
    6. protein binding Source: IntAct

    GO - Biological processi

    1. base-excision repair Source: InterPro

    Keywords - Molecular functioni

    Glycosidase, Hydrolase, Lyase

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    4Fe-4S, DNA-binding, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10662-MONOMER.
    ECOL316407:JW1625-MONOMER.
    MetaCyc:EG10662-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Endonuclease IIIUniRule annotation (EC:4.2.99.18UniRule annotation)
    Alternative name(s):
    DNA-(apurinic or apyrimidinic site) lyaseUniRule annotation
    Gene namesi
    Name:nthUniRule annotation
    Ordered Locus Names:b1633, JW1625
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10662. nth.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi120 – 1201K → Q: 100000-fold decrease in activity and slight decrease in substrate affinity. 1 Publication
    Mutagenesisi138 – 1381D → N: 100-fold decrease in activity and 4-fold increase in substrate affinity. 1 Publication
    Mutagenesisi191 – 1911K → E: Slight decrease in activity and 130-fold increase in substrate affinity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 211211Endonuclease IIIPRO_0000102210Add
    BLAST

    Expressioni

    Gene expression databases

    GenevestigatoriP0AB83.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    aceEP0AFG82EBI-555213,EBI-542683

    Protein-protein interaction databases

    DIPiDIP-48071N.
    IntActiP0AB83. 6 interactions.
    MINTiMINT-1223379.
    STRINGi511145.b1633.

    Structurei

    Secondary structure

    1
    211
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1614
    Helixi29 – 3810
    Turni39 – 413
    Helixi44 – 5411
    Turni55 – 573
    Helixi61 – 7616
    Helixi82 – 9817
    Turni99 – 1024
    Helixi108 – 1136
    Helixi119 – 13012
    Helixi139 – 14810
    Helixi156 – 16611
    Helixi169 – 1713
    Turni172 – 1743
    Helixi175 – 18511
    Beta strandi189 – 1913
    Helixi194 – 1963
    Helixi200 – 2023

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ABKX-ray1.85A1-211[»]
    ProteinModelPortaliP0AB83.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AB83.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini108 – 12720HhHUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the Nth/MutY family.UniRule annotation
    Contains 1 HhH domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0177.
    HOGENOMiHOG000252206.
    KOiK10773.
    OMAiDTHIYRV.
    OrthoDBiEOG6H4KC5.
    PhylomeDBiP0AB83.

    Family and domain databases

    Gene3Di1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    HAMAPiMF_00942. Nth.
    InterProiIPR011257. DNA_glycosylase.
    IPR004036. Endonuclease-III-like_CS2.
    IPR004035. Endouclease-III_FeS-bd_BS.
    IPR003651. Endouclease3_FeS-loop_motif.
    IPR003265. HhH-GPD_domain.
    IPR000445. HhH_motif.
    IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
    IPR023170. HTH_base_excis_C.
    IPR005759. Nth.
    [Graphical view]
    PfamiPF10576. EndIII_4Fe-2S. 1 hit.
    PF00633. HHH. 1 hit.
    PF00730. HhH-GPD. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001435. Nth. 1 hit.
    SMARTiSM00478. ENDO3c. 1 hit.
    SM00525. FES. 1 hit.
    SM00278. HhH1. 1 hit.
    [Graphical view]
    SUPFAMiSSF48150. SSF48150. 1 hit.
    TIGRFAMsiTIGR01083. nth. 1 hit.
    PROSITEiPS00764. ENDONUCLEASE_III_1. 1 hit.
    PS01155. ENDONUCLEASE_III_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0AB83-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNKAKRLEIL TRLRENNPHP TTELNFSSPF ELLIAVLLSA QATDVSVNKA    50
    TAKLYPVANT PAAMLELGVE GVKTYIKTIG LYNSKAENII KTCRILLEQH 100
    NGEVPEDRAA LEALPGVGRK TANVVLNTAF GWPTIAVDTH IFRVCNRTQF 150
    APGKNVEQVE EKLLKVVPAE FKVDCHHWLI LHGRYTCIAR KPRCGSCIIE 200
    DLCEYKEKVD I 211
    Length:211
    Mass (Da):23,562
    Last modified:November 8, 2005 - v1
    Checksum:iFF4245823B7F902B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02857 Genomic DNA. Translation: AAA24227.1.
    U00096 Genomic DNA. Translation: AAC74705.1.
    AP009048 Genomic DNA. Translation: BAA15387.1.
    PIRiA32412.
    RefSeqiNP_416150.1. NC_000913.3.
    YP_489897.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74705; AAC74705; b1633.
    BAA15387; BAA15387; BAA15387.
    GeneIDi12933192.
    947122.
    KEGGiecj:Y75_p1610.
    eco:b1633.
    PATRICi32118568. VBIEscCol129921_1704.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02857 Genomic DNA. Translation: AAA24227.1 .
    U00096 Genomic DNA. Translation: AAC74705.1 .
    AP009048 Genomic DNA. Translation: BAA15387.1 .
    PIRi A32412.
    RefSeqi NP_416150.1. NC_000913.3.
    YP_489897.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2ABK X-ray 1.85 A 1-211 [» ]
    ProteinModelPortali P0AB83.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48071N.
    IntActi P0AB83. 6 interactions.
    MINTi MINT-1223379.
    STRINGi 511145.b1633.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74705 ; AAC74705 ; b1633 .
    BAA15387 ; BAA15387 ; BAA15387 .
    GeneIDi 12933192.
    947122.
    KEGGi ecj:Y75_p1610.
    eco:b1633.
    PATRICi 32118568. VBIEscCol129921_1704.

    Organism-specific databases

    EchoBASEi EB0656.
    EcoGenei EG10662. nth.

    Phylogenomic databases

    eggNOGi COG0177.
    HOGENOMi HOG000252206.
    KOi K10773.
    OMAi DTHIYRV.
    OrthoDBi EOG6H4KC5.
    PhylomeDBi P0AB83.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10662-MONOMER.
    ECOL316407:JW1625-MONOMER.
    MetaCyc:EG10662-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0AB83.
    PROi P0AB83.

    Gene expression databases

    Genevestigatori P0AB83.

    Family and domain databases

    Gene3Di 1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    HAMAPi MF_00942. Nth.
    InterProi IPR011257. DNA_glycosylase.
    IPR004036. Endonuclease-III-like_CS2.
    IPR004035. Endouclease-III_FeS-bd_BS.
    IPR003651. Endouclease3_FeS-loop_motif.
    IPR003265. HhH-GPD_domain.
    IPR000445. HhH_motif.
    IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
    IPR023170. HTH_base_excis_C.
    IPR005759. Nth.
    [Graphical view ]
    Pfami PF10576. EndIII_4Fe-2S. 1 hit.
    PF00633. HHH. 1 hit.
    PF00730. HhH-GPD. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001435. Nth. 1 hit.
    SMARTi SM00478. ENDO3c. 1 hit.
    SM00525. FES. 1 hit.
    SM00278. HhH1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48150. SSF48150. 1 hit.
    TIGRFAMsi TIGR01083. nth. 1 hit.
    PROSITEi PS00764. ENDONUCLEASE_III_1. 1 hit.
    PS01155. ENDONUCLEASE_III_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Purification and characterization of Escherichia coli endonuclease III from the cloned nth gene."
      Asahara H., Wistort P.M., Bank J.F., Bakerian R.H., Cunningham R.P.
      Biochemistry 28:4444-4449(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, FUNCTION.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "DNA glycosylase activities for thymine residues damaged by ring saturation, fragmentation, or ring contraction are functions of endonuclease III in Escherichia coli."
      Breimer L.H., Lindahl T.
      J. Biol. Chem. 259:5543-5548(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
    6. "The mechanisms of action of E. coli endonuclease III and T4 UV endonuclease (endonuclease V) at AP sites."
      Kim J., Linn S.
      Nucleic Acids Res. 16:1135-1141(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    7. "Structure and function of Escherichia coli endonuclease III."
      Cunningham R.P., Ahern H., Xing D., Thayer M.M., Tainer J.A.
      Ann. N. Y. Acad. Sci. 726:215-222(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR.
    8. "Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III."
      Kuo C.-F., McRee D., Fisher C.L., O'Handley S.F., Cunningham R.P., Tainer J.A.
      Science 258:434-440(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
    9. "Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure."
      Thayer M.M., Ahern H., Xing D., Cunningham R.P., Tainer J.A.
      EMBO J. 14:4108-4120(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), COFACTOR, DNA-BINDING, MUTAGENESIS OF LYS-120; ASP-138 AND LYS-191.

    Entry informationi

    Entry nameiEND3_ECOLI
    AccessioniPrimary (citable) accession number: P0AB83
    Secondary accession number(s): P20625
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 8, 2005
    Last sequence update: November 8, 2005
    Last modified: October 1, 2014
    This is version 90 of the entry and version 1 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3