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Protein

Endonuclease III

Gene

nth

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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

[4Fe-4S] clusterUniRule annotationNote: 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

GO - Biological processi

Complete GO annotation...

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 Componenti: 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.Bsubs1_010100012286.

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.
InParanoidiP39788.
KOiK10773.
OMAiHHALILF.
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

        10         20         30         40         50
MLNLKQIEFC LDKIGDMFPH AECELVHSNP FELVVAVALS AQCTDALVNR
60 70 80 90 100
VTKTLFQKYK RPEDYLAVPL EELQQDIKSI GLYRNKAKNI QKLSKMIIED
110 120 130 140 150
YGGEVPRDRD ELVKLPGVGR KTANVVVSVA FGVPAIAVDT HVERVSKRLG
160 170 180 190 200
ICRWKDSVLE VEKTLMRKVP KEDWSVTHHR LIFFGRYHCK AQSPRCAECP
210
LLSLCREGQK RDKKGLVKR
Length:219
Mass (Da):25,000
Last modified:February 1, 1995 - v1
Checksum:iC38C66DA7948BA40
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_009967580.1. NZ_JNCM01000036.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_009967580.1. NZ_JNCM01000036.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012286.

Proteomic databases

PaxDbiP39788.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

GenoListiBSU22340. [Micado]

Phylogenomic databases

eggNOGiCOG0177.
HOGENOMiHOG000252208.
InParanoidiP39788.
KOiK10773.
OMAiHHALILF.
OrthoDBiEOG6H4KC5.
PhylomeDBiP39788.

Enzyme and pathway databases

BioCyciBSUB:BSU22340-MONOMER.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: July 22, 2015
This is version 123 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.