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Endonuclease III homolog (CeNTH) (EC 3.2.2.-) (EC 4.2.99.18) (Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase) (DNA glycosylase/AP lyase)

 NTH_CAEEL               Reviewed;         298 AA.
P54137; C7G4V3; D5MCR0; D5MCR1; D5MCR2;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
27-JUL-2011, sequence version 2.
28-FEB-2018, entry version 129.
RecName: Full=Endonuclease III homolog {ECO:0000255|HAMAP-Rule:MF_03183};
Short=CeNTH;
EC=3.2.2.- {ECO:0000255|HAMAP-Rule:MF_03183};
EC=4.2.99.18 {ECO:0000255|HAMAP-Rule:MF_03183};
AltName: Full=Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase {ECO:0000255|HAMAP-Rule:MF_03183};
Short=DNA glycosylase/AP lyase {ECO:0000255|HAMAP-Rule:MF_03183};
Name=nth-1 {ECO:0000255|HAMAP-Rule:MF_03183}; ORFNames=R10E4.5;
Caenorhabditis elegans.
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
NCBI_TaxID=6239;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM D), FUNCTION, BIOPHYSICOCHEMICAL
PROPERTIES, AND DISRUPTION PHENOTYPE.
PubMed=19481506; DOI=10.1016/j.dnarep.2009.04.020;
Morinaga H., Yonekura S., Nakamura N., Sugiyama H., Yonei S.,
Zhang-Akiyama Q.M.;
"Purification and characterization of Caenorhabditis elegans NTH, a
homolog of human endonuclease III: essential role of N-terminal
region.";
DNA Repair 8:844-851(2009).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE INITIATION,
AND ALTERNATIVE SPLICING.
STRAIN=Bristol N2;
PubMed=9851916; DOI=10.1126/science.282.5396.2012;
The C. elegans sequencing consortium;
"Genome sequence of the nematode C. elegans: a platform for
investigating biology.";
Science 282:2012-2018(1998).
[3]
DISRUPTION PHENOTYPE.
PubMed=16783005; DOI=10.1534/genetics.106.059840;
Denver D.R., Feinberg S., Steding C., Durbin M., Lynch M.;
"The relative roles of three DNA repair pathways in preventing
Caenorhabditis elegans mutation accumulation.";
Genetics 174:57-65(2006).
-!- 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. {ECO:0000255|HAMAP-Rule:MF_03183,
ECO:0000269|PubMed:19481506}.
-!- 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. {ECO:0000255|HAMAP-Rule:MF_03183}.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000255|HAMAP-Rule:MF_03183};
Note=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.
{ECO:0000255|HAMAP-Rule:MF_03183};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Temperature dependence:
Optimum temperature is 26 degrees Celsius.
{ECO:0000269|PubMed:19481506};
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03183}.
Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03183}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing, Alternative initiation; Named isoforms=4;
Name=d;
IsoId=P54137-1; Sequence=Displayed;
Name=a;
IsoId=P54137-2; Sequence=VSP_041641;
Note=Produced by alternative initiation.;
Name=b;
IsoId=P54137-3; Sequence=VSP_041642;
Note=Produced by alternative splicing.;
Name=c;
IsoId=P54137-4; Sequence=VSP_041643;
Note=Produced by alternative splicing.;
-!- DISRUPTION PHENOTYPE: 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.
{ECO:0000269|PubMed:16783005, ECO:0000269|PubMed:19481506}.
-!- SIMILARITY: Belongs to the Nth/MutY family. {ECO:0000255|HAMAP-
Rule:MF_03183}.
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EMBL; AB518695; BAI22676.1; -; mRNA.
EMBL; Z50874; CAA90766.2; -; Genomic_DNA.
EMBL; Z50874; CBK55598.1; -; Genomic_DNA.
EMBL; Z50874; CBK55599.1; -; Genomic_DNA.
EMBL; Z50874; CBK55600.1; -; Genomic_DNA.
PIR; T24131; T24131.
RefSeq; NP_001254906.1; NM_001267977.1. [P54137-1]
RefSeq; NP_001254907.1; NM_001267978.1. [P54137-2]
RefSeq; NP_001254908.1; NM_001267979.1. [P54137-3]
RefSeq; NP_001254909.1; NM_001267980.1. [P54137-4]
UniGene; Cel.10201; -.
UniGene; Cel.40199; -.
ProteinModelPortal; P54137; -.
SMR; P54137; -.
STRING; 6239.R10E4.5d; -.
PaxDb; P54137; -.
PeptideAtlas; P54137; -.
EnsemblMetazoa; R10E4.5d; R10E4.5d; WBGene00011201. [P54137-1]
GeneID; 187770; -.
KEGG; cel:CELE_R10E4.5; -.
CTD; 187770; -.
WormBase; R10E4.5a; CE44645; WBGene00011201; nth-1. [P54137-2]
WormBase; R10E4.5b; CE44659; WBGene00011201; nth-1. [P54137-3]
WormBase; R10E4.5c; CE44689; WBGene00011201; nth-1. [P54137-4]
WormBase; R10E4.5d; CE44095; WBGene00011201; nth-1. [P54137-1]
eggNOG; KOG1921; Eukaryota.
eggNOG; COG0177; LUCA.
GeneTree; ENSGT00510000047513; -.
HOGENOM; HOG000252209; -.
InParanoid; P54137; -.
KO; K10773; -.
OMA; KAKNPLC; -.
OrthoDB; EOG091G0IVB; -.
Reactome; R-CEL-110329; Cleavage of the damaged pyrimidine.
Reactome; R-CEL-110357; Displacement of DNA glycosylase by APEX1.
PRO; PR:P54137; -.
Proteomes; UP000001940; Chromosome III.
Bgee; WBGene00011201; -.
GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
GO; GO:0005634; C:nucleus; ISS:WormBase.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0034042; F:5-formyluracil DNA N-glycosylase activity; IDA:WormBase.
GO; GO:0034043; F:5-hydroxymethyluracil DNA N-glycosylase activity; IDA:WormBase.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) lyase activity; IEA:UniProtKB-EC.
GO; GO:0140080; F:class III/IV DNA-(apurinic or apyrimidinic site) lyase activity; IEA:UniProtKB-EC.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000703; F:oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity; IDA:WormBase.
GO; GO:0070301; P:cellular response to hydrogen peroxide; IGI:WormBase.
GO; GO:0045008; P:depyrimidination; IDA:WormBase.
GO; GO:0006281; P:DNA repair; IMP:WormBase.
GO; GO:0006296; P:nucleotide-excision repair, DNA incision, 5'-to lesion; IBA:GO_Central.
CDD; cd00056; ENDO3c; 1.
Gene3D; 1.10.1670.10; -; 1.
HAMAP; MF_03183; Endonuclease_III_Nth; 1.
InterPro; IPR011257; DNA_glycosylase.
InterPro; IPR004036; Endonuclease-III-like_CS2.
InterPro; IPR004035; Endouclease-III_FeS-bd_BS.
InterPro; IPR003265; HhH-GPD_domain.
InterPro; IPR000445; HhH_motif.
InterPro; IPR023170; HTH_base_excis_C.
InterPro; IPR030841; NTH1.
Pfam; PF00633; HHH; 1.
Pfam; PF00730; HhH-GPD; 1.
SMART; SM00478; ENDO3c; 1.
SUPFAM; SSF48150; SSF48150; 1.
PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
1: Evidence at protein level;
4Fe-4S; Alternative initiation; Alternative splicing;
Complete proteome; DNA damage; DNA repair; Glycosidase; Hydrolase;
Iron; Iron-sulfur; Lyase; Metal-binding; Mitochondrion; Nucleus;
Reference proteome.
CHAIN 1 298 Endonuclease III homolog.
/FTId=PRO_0000102229.
DOMAIN 138 165 HhH. {ECO:0000255|HAMAP-Rule:MF_03183}.
ACT_SITE 158 158 Nucleophile; for N-glycosylase activity.
{ECO:0000255|HAMAP-Rule:MF_03183}.
METAL 226 226 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
METAL 233 233 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
METAL 236 236 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
METAL 242 242 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
SITE 177 177 Important for catalytic activity.
{ECO:0000255|HAMAP-Rule:MF_03183}.
VAR_SEQ 1 158 Missing (in isoform c). {ECO:0000305}.
/FTId=VSP_041643.
VAR_SEQ 1 74 Missing (in isoform b). {ECO:0000305}.
/FTId=VSP_041642.
VAR_SEQ 1 5 Missing (in isoform a). {ECO:0000305}.
/FTId=VSP_041641.
SEQUENCE 298 AA; 33117 MW; ACD504175243F42A CRC64;
MHSFSMKRVV ASSSVAAVAT CDVEGTVVAW RRDVELIRKM RKDMIAPVDT MGCHKLADPL
AAPPVHRFQV LVALMLSSQT RDEVNAAAMK RLKDHGLSIG KILEFKVPDL ETILCPVGFY
KRKAVYLQKT AKILKDDFSG DIPDSLDGLC ALPGVGPKMA NLVMQIAWGE CVGIAVDTHV
HRISNRLGWI KTSTPEKTQK ALEILLPKSE WQPINHLLVG FGQMQCQPVR PKCGTCLCRF
TCPSSTAKNV KSETEETSTS IEVKQEVEDE FEDEKPAKKI KKTRKTRTKI EVKTESET


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