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Q09907

- NTH_SCHPO

UniProt

Q09907 - NTH_SCHPO

Protein

Endonuclease III homolog

Gene

nth1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 107 (01 Oct 2014)
      Sequence version 1 (01 Feb 1996)
      Previous versions | rss
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    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.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 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

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    2. 5-formyluracil DNA N-glycosylase activity Source: PomBase
    3. 5-hydroxymethyluracil DNA N-glycosylase activity Source: PomBase
    4. 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity Source: PomBase
    5. DNA binding Source: InterPro
    6. metal ion binding Source: UniProtKB-KW
    7. oxidized purine nucleobase lesion DNA N-glycosylase activity Source: PomBase
    8. oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Source: PomBase

    GO - Biological processi

    1. base-excision repair, AP site formation Source: PomBase
    2. DNA catabolic process, endonucleolytic Source: GOC

    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_220849. Recognition and association of DNA glycosylase with site containing an affected 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: Chromosome I

    Organism-specific databases

    PomBaseiSPAC30D11.07.

    Subcellular locationi

    Nucleus 2 PublicationsUniRule annotation. Mitochondrion UniRule annotation

    GO - Cellular componenti

    1. mitochondrial matrix Source: PomBase
    2. nucleus Source: PomBase

    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. 49 interactions.
    MINTiMINT-4696258.
    STRINGi4896.SPAC30D11.07-1.

    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.
    KOiK10773.
    OMAiPLWSEVN.
    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.
    [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

    MSKDYGTPPE NWREVYDEIC KMKAKVVAPV DVQGCHTLGE RNDPKKFRFQ    50
    TLVALMLSSQ TKDIVLGPTM RNLKEKLAGG LCLEDIQNID EVSLNKLIEK 100
    VGFHNRKTIY LKQMARILSE KFQGDIPDTV EDLMTLPGVG PKMGYLCMSI 150
    AWNKTVGIGV DVHVHRICNL LHWCNTKTEE QTRAALQSWL PKELWFELNH 200
    TLVGFGQTIC LPRGRRCDMC TLSSKGLCPS AFKEKSGITI TKRKVKTIKR 250
    VKKRPASESP PLSPLSLPTD DLYYQSIEDK SLIKLEDLDP VDSISHMNEP 300
    LKKEPAADID VDQKPPVAFH STTKETRSLR RSKRVAKKSS QYFSQQSLQD 350
    IEDLV 355
    Length:355
    Mass (Da):40,227
    Last modified:February 1, 1996 - v1
    Checksum:iD2E8C93A0DFA60EB
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB191154 mRNA. Translation: BAD93307.1 .
    CU329670 Genomic DNA. Translation: CAA91893.1 .
    PIRi JC6066. S62565.
    RefSeqi NP_593210.1. NM_001018606.2.

    3D structure databases

    ProteinModelPortali Q09907.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 279928. 49 interactions.
    MINTi MINT-4696258.
    STRINGi 4896.SPAC30D11.07-1.

    Proteomic databases

    MaxQBi Q09907.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii SPAC30D11.07.1 ; SPAC30D11.07.1:pep ; SPAC30D11.07 .
    GeneIDi 2543510.
    KEGGi spo:SPAC30D11.07.

    Organism-specific databases

    PomBasei SPAC30D11.07.

    Phylogenomic databases

    eggNOGi COG0177.
    HOGENOMi HOG000252209.
    KOi K10773.
    OMAi PLWSEVN.
    OrthoDBi EOG7PK99N.
    PhylomeDBi Q09907.

    Enzyme and pathway databases

    Reactomei REACT_220849. Recognition and association of DNA glycosylase with site containing an affected pyrimidine.

    Miscellaneous databases

    NextBioi 20804520.
    PROi Q09907.

    Family and domain databases

    Gene3Di 1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    HAMAPi MF_03183. Endonuclease_III_Nth.
    InterProi IPR011257. DNA_glycosylase.
    IPR004036. Endonuclease-III-like_CS2.
    IPR003651. Endouclease3_FeS-loop_motif.
    IPR003265. HhH-GPD_domain.
    IPR000445. HhH_motif.
    IPR023170. HTH_base_excis_C.
    [Graphical view ]
    Pfami PF00633. HHH. 1 hit.
    PF00730. HhH-GPD. 1 hit.
    [Graphical view ]
    SMARTi SM00478. ENDO3c. 1 hit.
    SM00525. FES. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48150. SSF48150. 1 hit.
    PROSITEi PS01155. ENDONUCLEASE_III_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 107 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