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P39788

- END3_BACSU

UniProt

P39788 - END3_BACSU

Protein

Endonuclease III

Gene

nth

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      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.UniRule 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.UniRule annotation

    Cofactori

    Binds 1 4Fe-4S cluster.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi189 – 1891Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi196 – 1961Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi199 – 1991Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi205 – 2051Iron-sulfur (4Fe-4S)UniRule annotation

    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

    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

    BioCyciBSUB:BSU22340-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
    Synonyms:jooB, ypoB
    Ordered Locus Names:BSU22340
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU22340. [Micado]

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene have a 5-fold increased spontaneous mutation frequency. A triple MutS/MutL/nth disruption has a 280-fold increased spontaneous mutation frequency.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 219219Endonuclease IIIPRO_0000102213Add
    BLAST

    Proteomic databases

    PaxDbiP39788.

    Interactioni

    Protein-protein interaction databases

    STRINGi224308.BSU22340.

    Structurei

    3D structure databases

    ProteinModelPortaliP39788.
    SMRiP39788. Positions 1-211.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini109 – 12820HhHUniRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0177.
    HOGENOMiHOG000252208.
    KOiK10773.
    OMAiDTHIYRV.
    OrthoDBiEOG6H4KC5.
    PhylomeDBiP39788.

    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]
    PfamiPF00633. 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.

    P39788-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLNLKQIEFC LDKIGDMFPH AECELVHSNP FELVVAVALS AQCTDALVNR    50
    VTKTLFQKYK RPEDYLAVPL EELQQDIKSI GLYRNKAKNI QKLSKMIIED 100
    YGGEVPRDRD ELVKLPGVGR KTANVVVSVA FGVPAIAVDT HVERVSKRLG 150
    ICRWKDSVLE VEKTLMRKVP KEDWSVTHHR LIFFGRYHCK AQSPRCAECP 200
    LLSLCREGQK RDKKGLVKR 219
    Length:219
    Mass (Da):25,000
    Last modified:February 1, 1995 - v1
    Checksum:iC38C66DA7948BA40
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U11289 Genomic DNA. Translation: AAA80005.1.
    L47709 Genomic DNA. Translation: AAB38457.1.
    AL009126 Genomic DNA. Translation: CAB14150.1.
    PIRiI40525.
    RefSeqiNP_390115.1. NC_000964.3.

    Genome annotation databases

    EnsemblBacteriaiCAB14150; CAB14150; BSU22340.
    GeneIDi939036.
    KEGGibsu:BSU22340.
    PATRICi18976277. VBIBacSub10457_2329.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U11289 Genomic DNA. Translation: AAA80005.1 .
    L47709 Genomic DNA. Translation: AAB38457.1 .
    AL009126 Genomic DNA. Translation: CAB14150.1 .
    PIRi I40525.
    RefSeqi NP_390115.1. NC_000964.3.

    3D structure databases

    ProteinModelPortali P39788.
    SMRi P39788. Positions 1-211.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU22340.

    Proteomic databases

    PaxDbi P39788.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB14150 ; CAB14150 ; BSU22340 .
    GeneIDi 939036.
    KEGGi bsu:BSU22340.
    PATRICi 18976277. VBIBacSub10457_2329.

    Organism-specific databases

    GenoListi BSU22340. [Micado ]

    Phylogenomic databases

    eggNOGi COG0177.
    HOGENOMi HOG000252208.
    KOi K10773.
    OMAi DTHIYRV.
    OrthoDBi EOG6H4KC5.
    PhylomeDBi P39788.

    Enzyme and pathway databases

    BioCyci BSUB:BSU22340-MONOMER.

    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 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. "Nucleotide sequence of the Bacillus subtilis dnaD gene."
      Bruand C., Sorokin A., Serror P., Ehrlich S.D.
      Microbiology 141:321-322(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "Sequence analysis of the Bacillus subtilis chromosome region between the serA and kdg loci cloned in a yeast artificial chromosome."
      Sorokin A.V., Azevedo V., Zumstein E., Galleron N., Ehrlich S.D., Serror P.
      Microbiology 142:2005-2016(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    4. "Genetic analysis of Bacillus subtilis mutator genes."
      Sasaki M., Yonemura Y., Kurusu Y.
      J. Gen. Appl. Microbiol. 46:183-187(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
      Strain: 168.

    Entry informationi

    Entry nameiEND3_BACSU
    AccessioniPrimary (citable) accession number: P39788
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 117 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

    Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3