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Q09907 (NTH_SCHPO) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Endonuclease III homolog

EC=3.2.2.-
EC=4.2.99.18
Alternative name(s):
Bifunctional DNA N-glycoslyase/DNA-(apurinic or apyrimidinic site) lyase
Short name=DNA glycoslyase/AP lyase
Gene names
Name:nth1
ORF Names:SPAC30D11.07
OrganismSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) [Reference proteome]
Taxonomic identifier284812 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces

Protein attributes

Sequence length355 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.3 Ref.4 Ref.5 Ref.7

Catalytic activity

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. Ref.4

Cofactor

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 By similarity.

Subcellular location

Nucleus. Mitochondrion By similarity Ref.1 Ref.6.

Sequence similarities

Belongs to the Nth/MutY family.

Contains 1 HhH domain.

Biophysicochemical properties

Kinetic parameters:

KM=963 nM for 5-hydroxy-6-hydrothymine containing duplex oligonucleotides (N-glycosylase activity) Ref.4

KM=173 nM for 5-hydroxyuracil containing duplex oligonucleotides (N-glycosylase activity)

KM=360 nM for 5-hydroxycytosine containing duplex oligonucleotides (N-glycosylase activity)

KM=1741 nM for thymine glycol containing duplex oligonucleotides (N-glycosylase activity)

KM=111 nM for 5,6-dihydroxycytosine containing duplex oligonucleotides (N-glycosylase activity)

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 355355Endonuclease III homolog HAMAP-Rule MF_03183
PRO_0000102226

Regions

Domain122 – 14928HhH
Motif44 – 507Nuclear localization signal Potential
Motif252 – 2554Nuclear localization signal Potential

Sites

Active site1421Nucleophile; for N-glycosylase activity By similarity
Metal binding2101Iron-sulfur (4Fe-4S) By similarity
Metal binding2171Iron-sulfur (4Fe-4S) By similarity
Metal binding2201Iron-sulfur (4Fe-4S) By similarity
Metal binding2281Iron-sulfur (4Fe-4S) By similarity
Site1611Important for catalytic activity By similarity

Sequences

Sequence LengthMass (Da)Tools
Q09907 [UniParc].

Last modified February 1, 1996. Version 1.
Checksum: D2E8C93A0DFA60EB

FASTA35540,227
        10         20         30         40         50         60 
MSKDYGTPPE NWREVYDEIC KMKAKVVAPV DVQGCHTLGE RNDPKKFRFQ TLVALMLSSQ 

        70         80         90        100        110        120 
TKDIVLGPTM RNLKEKLAGG LCLEDIQNID EVSLNKLIEK VGFHNRKTIY LKQMARILSE 

       130        140        150        160        170        180 
KFQGDIPDTV EDLMTLPGVG PKMGYLCMSI AWNKTVGIGV DVHVHRICNL LHWCNTKTEE 

       190        200        210        220        230        240 
QTRAALQSWL PKELWFELNH TLVGFGQTIC LPRGRRCDMC TLSSKGLCPS AFKEKSGITI 

       250        260        270        280        290        300 
TKRKVKTIKR VKKRPASESP PLSPLSLPTD DLYYQSIEDK SLIKLEDLDP VDSISHMNEP 

       310        320        330        340        350 
LKKEPAADID VDQKPPVAFH STTKETRSLR RSKRVAKKSS QYFSQQSLQD IEDLV 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB191154 mRNA. Translation: BAD93307.1.
CU329670 Genomic DNA. Translation: CAA91893.1.
PIRS62565. JC6066.
RefSeqNP_593210.1. NM_001018606.2.

3D structure databases

ProteinModelPortalQ09907.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid279928. 49 interactions.
MINTMINT-4696258.
STRING4896.SPAC30D11.07-1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiSPAC30D11.07.1; SPAC30D11.07.1:pep; SPAC30D11.07.
GeneID2543510.
KEGGspo:SPAC30D11.07.

Organism-specific databases

PomBaseSPAC30D11.07.

Phylogenomic databases

eggNOGCOG0177.
HOGENOMHOG000252209.
KOK10773.
OMAHEMVENE.
OrthoDBEOG7PK99N.
PhylomeDBQ09907.

Family and domain databases

Gene3D1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPMF_03183. Endonuclease_III_Nth.
InterProIPR011257. 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]
PfamPF00633. HHH. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view]
SMARTSM00478. ENDO3c. 1 hit.
SM00525. FES. 1 hit.
[Graphical view]
SUPFAMSSF48150. SSF48150. 1 hit.
PROSITEPS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio20804520.
PROQ09907.

Entry information

Entry nameNTH_SCHPO
AccessionPrimary (citable) accession number: Q09907
Secondary accession number(s): Q588X4
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: April 16, 2014
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Schizosaccharomyces pombe

Schizosaccharomyces pombe: entries and gene names