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Protein

Endonuclease III homolog

Gene

nth1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Bifunctional DNA N-glycosylase with associated apurinic/apyrimidinic (AP) lyase function that catalyzes the first step in base excision repair (BER), the primary repair pathway for the repair of oxidative DNA damage. The DNA N-glycosylase activity releases the damaged DNA base from DNA by cleaving the N-glycosidic bond, leaving an AP site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination. Primarily recognizes and repairs oxidative base damage of pyrimidines. Has also 8-oxo-7,8-dihydroguanine (8-oxoG) DNA glycosylase activity. Also involved in the repair of 7-methylguanine lesions, although it cannot directly repair alkylated DNA bases. Probably does so via excision of methylformamidopyrimidine (mFapy) lesions, a spontaneous processing product of 7-methylguanine.5 Publications

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 annotation1 Publication

Cofactori

[4Fe-4S] clusterUniRule annotationNote: Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a role in catalysis, but is probably involved in the proper positioning of the enzyme along the DNA strand.UniRule annotation

Kineticsi

  1. KM=963 nM for 5-hydroxy-6-hydrothymine containing duplex oligonucleotides (N-glycosylase activity)1 Publication
  2. KM=173 nM for 5-hydroxyuracil containing duplex oligonucleotides (N-glycosylase activity)1 Publication
  3. KM=360 nM for 5-hydroxycytosine containing duplex oligonucleotides (N-glycosylase activity)1 Publication
  4. KM=1741 nM for thymine glycol containing duplex oligonucleotides (N-glycosylase activity)1 Publication
  5. KM=111 nM for 5,6-dihydroxycytosine containing duplex oligonucleotides (N-glycosylase activity)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei142 – 1421Nucleophile; for N-glycosylase activityUniRule annotation
    Sitei161 – 1611Important for catalytic activityUniRule annotation
    Metal bindingi210 – 2101Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi217 – 2171Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi220 – 2201Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi228 – 2281Iron-sulfur (4Fe-4S)UniRule annotation

    GO - Molecular functioni

    • 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
    • 5-formyluracil DNA N-glycosylase activity Source: PomBase
    • 5-hydroxymethyluracil DNA N-glycosylase activity Source: PomBase
    • 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity Source: PomBase
    • DNA binding Source: UniProtKB-HAMAP
    • metal ion binding Source: UniProtKB-KW
    • oxidized purine nucleobase lesion DNA N-glycosylase activity Source: PomBase
    • oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Source: PomBase

    GO - Biological processi

    • base-excision repair, AP site formation Source: PomBase
    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase, Lyase

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

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

    Enzyme and pathway databases

    ReactomeiREACT_348086. Cleavage of the damaged pyrimidine.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Endonuclease III homologUniRule annotation (EC:3.2.2.-UniRule annotation, EC:4.2.99.18UniRule annotation)
    Alternative name(s):
    Bifunctional DNA N-glycoslyase/DNA-(apurinic or apyrimidinic site) lyaseUniRule annotation
    Short name:
    DNA glycoslyase/AP lyaseUniRule annotation
    Gene namesi
    Name:nth1
    ORF Names:SPAC30D11.07
    OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
    Taxonomic identifieri284812 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
    ProteomesiUP000002485 Componenti: Chromosome I

    Organism-specific databases

    EuPathDBiFungiDB:SPAC30D11.07.
    PomBaseiSPAC30D11.07. nth1.

    Subcellular locationi

    GO - Cellular componenti

    • mitochondrial matrix Source: PomBase
    • nucleus Source: PomBase
    Complete GO annotation...

    Keywords - Cellular componenti

    Mitochondrion, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 355355Endonuclease III homologPRO_0000102226Add
    BLAST

    Proteomic databases

    MaxQBiQ09907.

    Interactioni

    Protein-protein interaction databases

    BioGridi279928. 50 interactions.
    MINTiMINT-4696258.

    Structurei

    3D structure databases

    ProteinModelPortaliQ09907.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini122 – 14928HhHUniRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi44 – 507Nuclear localization signalSequence Analysis
    Motifi252 – 2554Nuclear localization signalSequence Analysis

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0177.
    HOGENOMiHOG000252209.
    InParanoidiQ09907.
    KOiK10773.
    OMAiISHMNEP.
    OrthoDBiEOG7PK99N.
    PhylomeDBiQ09907.

    Family and domain databases

    Gene3Di1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    HAMAPiMF_03183. Endonuclease_III_Nth.
    InterProiIPR011257. DNA_glycosylase.
    IPR004036. Endonuclease-III-like_CS2.
    IPR003651. Endouclease3_FeS-loop_motif.
    IPR003265. HhH-GPD_domain.
    IPR000445. HhH_motif.
    IPR023170. HTH_base_excis_C.
    IPR030841. NTH1.
    [Graphical view]
    PfamiPF00633. HHH. 1 hit.
    PF00730. HhH-GPD. 1 hit.
    [Graphical view]
    SMARTiSM00478. ENDO3c. 1 hit.
    SM00525. FES. 1 hit.
    [Graphical view]
    SUPFAMiSSF48150. SSF48150. 1 hit.
    PROSITEiPS01155. ENDONUCLEASE_III_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q09907-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKDYGTPPE NWREVYDEIC KMKAKVVAPV DVQGCHTLGE RNDPKKFRFQ
    60 70 80 90 100
    TLVALMLSSQ TKDIVLGPTM RNLKEKLAGG LCLEDIQNID EVSLNKLIEK
    110 120 130 140 150
    VGFHNRKTIY LKQMARILSE KFQGDIPDTV EDLMTLPGVG PKMGYLCMSI
    160 170 180 190 200
    AWNKTVGIGV DVHVHRICNL LHWCNTKTEE QTRAALQSWL PKELWFELNH
    210 220 230 240 250
    TLVGFGQTIC LPRGRRCDMC TLSSKGLCPS AFKEKSGITI TKRKVKTIKR
    260 270 280 290 300
    VKKRPASESP PLSPLSLPTD DLYYQSIEDK SLIKLEDLDP VDSISHMNEP
    310 320 330 340 350
    LKKEPAADID VDQKPPVAFH STTKETRSLR RSKRVAKKSS QYFSQQSLQD

    IEDLV
    Length:355
    Mass (Da):40,227
    Last modified:February 1, 1996 - v1
    Checksum:iD2E8C93A0DFA60EB
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB191154 mRNA. Translation: BAD93307.1.
    CU329670 Genomic DNA. Translation: CAA91893.1.
    PIRiJC6066. S62565.
    RefSeqiNP_593210.1. NM_001018606.2.

    Genome annotation databases

    EnsemblFungiiSPAC30D11.07.1; SPAC30D11.07.1:pep; SPAC30D11.07.
    GeneIDi2543510.
    KEGGispo:SPAC30D11.07.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB191154 mRNA. Translation: BAD93307.1.
    CU329670 Genomic DNA. Translation: CAA91893.1.
    PIRiJC6066. S62565.
    RefSeqiNP_593210.1. NM_001018606.2.

    3D structure databases

    ProteinModelPortaliQ09907.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi279928. 50 interactions.
    MINTiMINT-4696258.

    Proteomic databases

    MaxQBiQ09907.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiSPAC30D11.07.1; SPAC30D11.07.1:pep; SPAC30D11.07.
    GeneIDi2543510.
    KEGGispo:SPAC30D11.07.

    Organism-specific databases

    EuPathDBiFungiDB:SPAC30D11.07.
    PomBaseiSPAC30D11.07. nth1.

    Phylogenomic databases

    eggNOGiCOG0177.
    HOGENOMiHOG000252209.
    InParanoidiQ09907.
    KOiK10773.
    OMAiISHMNEP.
    OrthoDBiEOG7PK99N.
    PhylomeDBiQ09907.

    Enzyme and pathway databases

    ReactomeiREACT_348086. Cleavage of the damaged pyrimidine.

    Miscellaneous databases

    NextBioi20804520.
    PROiQ09907.

    Family and domain databases

    Gene3Di1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    HAMAPiMF_03183. Endonuclease_III_Nth.
    InterProiIPR011257. DNA_glycosylase.
    IPR004036. Endonuclease-III-like_CS2.
    IPR003651. Endouclease3_FeS-loop_motif.
    IPR003265. HhH-GPD_domain.
    IPR000445. HhH_motif.
    IPR023170. HTH_base_excis_C.
    IPR030841. NTH1.
    [Graphical view]
    PfamiPF00633. HHH. 1 hit.
    PF00730. HhH-GPD. 1 hit.
    [Graphical view]
    SMARTiSM00478. ENDO3c. 1 hit.
    SM00525. FES. 1 hit.
    [Graphical view]
    SUPFAMiSSF48150. SSF48150. 1 hit.
    PROSITEiPS01155. ENDONUCLEASE_III_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Roles of base excision repair enzymes Nth1p and Apn2p from Schizosaccharomyces pombe in processing alkylation and oxidative DNA damage."
      Sugimoto T., Igawa E., Tanihigashi H., Matsubara M., Ide H., Ikeda S.
      DNA Repair 4:1270-1280(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION.
    2. "The genome sequence of Schizosaccharomyces pombe."
      Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
      , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
      Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 972 / ATCC 24843.
    3. "Molecular cloning and functional analysis of a Schizosaccharomyces pombe homologue of Escherichia coli endonuclease III."
      Roldan-Arjona T., Anselmino C., Lindahl T.
      Nucleic Acids Res. 24:3307-3312(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBSTRATES.
    4. "Substrate specificity of Schizosaccharomyces pombe Nth protein for products of oxidative DNA damage."
      Karahalil B., Roldan-Arjona T., Dizdaroglu M.
      Biochemistry 37:590-595(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    5. "A new Schizosaccharomyces pombe base excision repair mutant, nth1, reveals overlapping pathways for repair of DNA base damage."
      Osman F., Bjoras M., Alseth I., Morland I., McCready S., Seeberg E., Tsaneva I.
      Mol. Microbiol. 48:465-480(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MMS-DAMAGE REPAIR.
    6. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
      Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
      Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    7. "Recombinant Schizosaccharomyces pombe Nth1 protein exhibits DNA glycosylase activities for 8-oxo-7,8-dihydroguanine and thymine residues oxidized in the methyl group."
      Yonekura S., Nakamura N., Doi T., Sugiyama H., Yamamoto K., Yonei S., Zhang Q.M.
      J. Radiat. Res. 48:417-424(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBSTRATES.

    Entry informationi

    Entry nameiNTH_SCHPO
    AccessioniPrimary (citable) accession number: Q09907
    Secondary accession number(s): Q588X4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: February 1, 1996
    Last modified: July 22, 2015
    This is version 115 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Schizosaccharomyces pombe
      Schizosaccharomyces pombe: entries and gene names
    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.