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P54137

- NTH_CAEEL

UniProt

P54137 - NTH_CAEEL

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Protein

Endonuclease III homolog

Gene

nth-1

Organism
Caenorhabditis elegans
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.1 PublicationUniRule 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

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

Temperature dependencei

Optimum temperature is 26 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei158 – 1581Nucleophile; for N-glycosylase activityUniRule annotation
Sitei177 – 1771Important for catalytic activityUniRule annotation
Metal bindingi226 – 2261Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi233 – 2331Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi236 – 2361Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi242 – 2421Iron-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: WormBase
  3. 5-hydroxymethyluracil DNA N-glycosylase activity Source: WormBase
  4. DNA binding Source: InterPro
  5. metal ion binding Source: UniProtKB-KW
  6. oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Source: WormBase

GO - Biological processi

  1. cellular response to hydrogen peroxide Source: WormBase
  2. depyrimidination Source: WormBase
  3. DNA catabolic process, endonucleolytic Source: GOC
  4. DNA repair Source: WormBase
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

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease III homologUniRule annotation (EC:3.2.2.-UniRule annotation, EC:4.2.99.18UniRule annotation)
Short name:
CeNTH
Alternative name(s):
Bifunctional DNA N-glycoslyase/DNA-(apurinic or apyrimidinic site) lyaseUniRule annotation
Short name:
DNA glycoslyase/AP lyaseUniRule annotation
Gene namesi
Name:nth-1UniRule annotation
ORF Names:R10E4.5
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
ProteomesiUP000001940: Chromosome III

Organism-specific databases

WormBaseiR10E4.5a; CE44645; WBGene00011201; nth-1.
R10E4.5b; CE44659; WBGene00011201; nth-1.
R10E4.5c; CE44689; WBGene00011201; nth-1.
R10E4.5d; CE44095; WBGene00011201; nth-1.

Subcellular locationi

Nucleus UniRule annotation. Mitochondrion UniRule annotation

GO - Cellular componenti

  1. mitochondrion Source: UniProtKB-KW
  2. nucleus Source: WormBase
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

Pathology & Biotechi

Disruption phenotypei

Increases the total average mutation rate 17-fold. No significant abnormality in lifespan or sensitivity to oxidizing agents such as hydrogen peroxide and methyl viologen (MV); due to the redundancy with other DNA glycosylases.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 298298Endonuclease III homologPRO_0000102229Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi6239.R10E4.5.

Structurei

3D structure databases

ProteinModelPortaliP54137.
SMRiP54137. Positions 65-239.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini138 – 16528HhHUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0177.
GeneTreeiENSGT00510000047513.
HOGENOMiHOG000252209.
InParanoidiP54137.
OMAiWRNKVKY.
OrthoDBiEOG76MK8Z.

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.
IPR004035. Endouclease-III_FeS-bd_BS.
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.
PROSITEiPS00764. ENDONUCLEASE_III_1. 1 hit.
PS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing and alternative initiation. Align

Isoform d (identifier: P54137) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MHSFSMKRVV ASSSVAAVAT CDVEGTVVAW RRDVELIRKM RKDMIAPVDT
60 70 80 90 100
MGCHKLADPL AAPPVHRFQV LVALMLSSQT RDEVNAAAMK RLKDHGLSIG
110 120 130 140 150
KILEFKVPDL ETILCPVGFY KRKAVYLQKT AKILKDDFSG DIPDSLDGLC
160 170 180 190 200
ALPGVGPKMA NLVMQIAWGE CVGIAVDTHV HRISNRLGWI KTSTPEKTQK
210 220 230 240 250
ALEILLPKSE WQPINHLLVG FGQMQCQPVR PKCGTCLCRF TCPSSTAKNV
260 270 280 290
KSETEETSTS IEVKQEVEDE FEDEKPAKKI KKTRKTRTKI EVKTESET
Length:298
Mass (Da):33,117
Last modified:July 27, 2011 - v2
Checksum:iACD504175243F42A
GO
Isoform a (identifier: P54137-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-5: Missing.

Note: Produced by alternative initiation.

Show »
Length:293
Mass (Da):32,527
Checksum:i1FF1D1B8626B6B8E
GO
Isoform b (identifier: P54137-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-74: Missing.

Note: Produced by alternative splicing.

Show »
Length:224
Mass (Da):25,017
Checksum:i25407C4744713639
GO
Isoform c (identifier: P54137-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-158: Missing.

Note: Produced by alternative splicing.

Show »
Length:140
Mass (Da):15,858
Checksum:iBB4A45A3DC81D3CD
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 158158Missing in isoform c. CuratedVSP_041643Add
BLAST
Alternative sequencei1 – 7474Missing in isoform b. CuratedVSP_041642Add
BLAST
Alternative sequencei1 – 55Missing in isoform a. CuratedVSP_041641

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB518695 mRNA. Translation: BAI22676.1.
Z50874 Genomic DNA. Translation: CAA90766.2.
Z50874 Genomic DNA. Translation: CBK55598.1.
Z50874 Genomic DNA. Translation: CBK55599.1.
Z50874 Genomic DNA. Translation: CBK55600.1.
PIRiT24131.
RefSeqiNP_001254906.1. NM_001267977.1. [P54137-1]
NP_001254907.1. NM_001267978.1. [P54137-2]
NP_001254908.1. NM_001267979.1. [P54137-3]
NP_001254909.1. NM_001267980.1. [P54137-4]
UniGeneiCel.10201.
Cel.40199.

Genome annotation databases

EnsemblMetazoaiR10E4.5d; R10E4.5d; WBGene00011201. [P54137-1]
GeneIDi187770.
KEGGicel:CELE_R10E4.5.

Keywords - Coding sequence diversityi

Alternative initiation, Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB518695 mRNA. Translation: BAI22676.1 .
Z50874 Genomic DNA. Translation: CAA90766.2 .
Z50874 Genomic DNA. Translation: CBK55598.1 .
Z50874 Genomic DNA. Translation: CBK55599.1 .
Z50874 Genomic DNA. Translation: CBK55600.1 .
PIRi T24131.
RefSeqi NP_001254906.1. NM_001267977.1. [P54137-1 ]
NP_001254907.1. NM_001267978.1. [P54137-2 ]
NP_001254908.1. NM_001267979.1. [P54137-3 ]
NP_001254909.1. NM_001267980.1. [P54137-4 ]
UniGenei Cel.10201.
Cel.40199.

3D structure databases

ProteinModelPortali P54137.
SMRi P54137. Positions 65-239.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 6239.R10E4.5.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblMetazoai R10E4.5d ; R10E4.5d ; WBGene00011201 . [P54137-1 ]
GeneIDi 187770.
KEGGi cel:CELE_R10E4.5.

Organism-specific databases

CTDi 187770.
WormBasei R10E4.5a ; CE44645 ; WBGene00011201 ; nth-1.
R10E4.5b ; CE44659 ; WBGene00011201 ; nth-1.
R10E4.5c ; CE44689 ; WBGene00011201 ; nth-1.
R10E4.5d ; CE44095 ; WBGene00011201 ; nth-1.

Phylogenomic databases

eggNOGi COG0177.
GeneTreei ENSGT00510000047513.
HOGENOMi HOG000252209.
InParanoidi P54137.
OMAi WRNKVKY.
OrthoDBi EOG76MK8Z.

Miscellaneous databases

NextBioi 936446.
PROi P54137.

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.
IPR004035. Endouclease-III_FeS-bd_BS.
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 PS00764. ENDONUCLEASE_III_1. 1 hit.
PS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Purification and characterization of Caenorhabditis elegans NTH, a homolog of human endonuclease III: essential role of N-terminal region."
    Morinaga H., Yonekura S., Nakamura N., Sugiyama H., Yonei S., Zhang-Akiyama Q.M.
    DNA Repair 8:844-851(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM D), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, DISRUPTION PHENOTYPE.
  2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE INITIATION, ALTERNATIVE SPLICING.
    Strain: Bristol N2.
  3. "The relative roles of three DNA repair pathways in preventing Caenorhabditis elegans mutation accumulation."
    Denver D.R., Feinberg S., Steding C., Durbin M., Lynch M.
    Genetics 174:57-65(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiNTH_CAEEL
AccessioniPrimary (citable) accession number: P54137
Secondary accession number(s): C7G4V3
, D5MCR0, D5MCR1, D5MCR2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: July 27, 2011
Last modified: October 29, 2014
This is version 107 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3