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Q09907

- NTH_SCHPO

UniProt

Q09907 - NTH_SCHPO

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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

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
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_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
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.
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.
InParanoidiQ09907.
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

        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:
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. 50 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.
InParanoidi Q09907.
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

« 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: October 29, 2014
This is version 108 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