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Endonuclease III homolog 1, chloroplastic (AtNTH1) (EC 3.2.2.-) (EC 4.2.99.18) (Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase 1) (DNA glycosylase/AP lyase 1)

 NTH1_ARATH              Reviewed;         379 AA.
Q9SIC4; Q8LF57; Q8VZT5; Q9FT83;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
01-JUN-2002, sequence version 2.
10-OCT-2018, entry version 119.
RecName: Full=Endonuclease III homolog 1, chloroplastic {ECO:0000255|HAMAP-Rule:MF_03183};
Short=AtNTH1;
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 1 {ECO:0000255|HAMAP-Rule:MF_03183};
Short=DNA glycosylase/AP lyase 1 {ECO:0000255|HAMAP-Rule:MF_03183};
Flags: Precursor;
Name=NTH1 {ECO:0000255|HAMAP-Rule:MF_03183};
OrderedLocusNames=At2g31450; ORFNames=T28P16.6;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [MRNA] OF 18-379, FUNCTION, AND TISSUE
SPECIFICITY.
STRAIN=cv. Columbia;
PubMed=11094978; DOI=10.1023/A:1006429114451;
Roldan-Arjona T., Garcia-Ortiz M.V., Ruiz-Rubio M., Ariza R.R.;
"cDNA cloning, expression and functional characterization of an
Arabidopsis thaliana homologue of the Escherichia coli DNA repair
enzyme endonuclease III.";
Plant Mol. Biol. 44:43-52(2000).
[6]
DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
STRAIN=cv. Columbia;
PubMed=19372224; DOI=10.1074/jbc.M109.008342;
Gutman B.L., Niyogi K.K.;
"Evidence for base excision repair of oxidative DNA damage in
chloroplasts of Arabidopsis thaliana.";
J. Biol. Chem. 284:17006-17012(2009).
-!- 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:11094978}.
-!- 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};
-!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma, chloroplast
nucleoid {ECO:0000269|PubMed:19372224}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9SIC4-1; Sequence=Displayed;
Name=2;
IsoId=Q9SIC4-2; Sequence=VSP_053921;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Expressed at low levels in roots, stems,
leaves and flowers. {ECO:0000269|PubMed:11094978}.
-!- DISRUPTION PHENOTYPE: No effect on chloroplastic glycosylase-
lyase/endonuclease activity, probably due to function redundancy.
{ECO:0000269|PubMed:19372224}.
-!- SIMILARITY: Belongs to the Nth/MutY family. {ECO:0000255|HAMAP-
Rule:MF_03183}.
-!- SEQUENCE CAUTION:
Sequence=CAC16135.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AC007169; AAD26474.2; -; Genomic_DNA.
EMBL; CP002685; AEC08549.1; -; Genomic_DNA.
EMBL; CP002685; AEC08550.1; -; Genomic_DNA.
EMBL; AY063851; AAL36207.1; -; mRNA.
EMBL; AY091229; AAM14168.1; -; mRNA.
EMBL; AY085041; AAM61598.1; -; mRNA.
EMBL; AJ272248; CAC16135.1; ALT_INIT; mRNA.
PIR; H84720; H84720.
RefSeq; NP_001077988.1; NM_001084519.1. [Q9SIC4-2]
RefSeq; NP_565725.1; NM_128702.3. [Q9SIC4-1]
UniGene; At.10180; -.
ProteinModelPortal; Q9SIC4; -.
SMR; Q9SIC4; -.
STRING; 3702.AT2G31450.1; -.
iPTMnet; Q9SIC4; -.
PaxDb; Q9SIC4; -.
EnsemblPlants; AT2G31450.1; AT2G31450.1; AT2G31450. [Q9SIC4-1]
EnsemblPlants; AT2G31450.2; AT2G31450.2; AT2G31450. [Q9SIC4-2]
GeneID; 817703; -.
Gramene; AT2G31450.1; AT2G31450.1; AT2G31450. [Q9SIC4-1]
Gramene; AT2G31450.2; AT2G31450.2; AT2G31450. [Q9SIC4-2]
KEGG; ath:AT2G31450; -.
Araport; AT2G31450; -.
TAIR; locus:2061345; AT2G31450.
eggNOG; KOG1921; Eukaryota.
eggNOG; COG0177; LUCA.
HOGENOM; HOG000252209; -.
InParanoid; Q9SIC4; -.
KO; K10773; -.
OMA; NLCPSAF; -.
OrthoDB; EOG09360EOS; -.
PhylomeDB; Q9SIC4; -.
BRENDA; 4.2.99.18; 399.
Reactome; R-ATH-110329; Cleavage of the damaged pyrimidine.
Reactome; R-ATH-110357; Displacement of DNA glycosylase by APEX1.
PRO; PR:Q9SIC4; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; Q9SIC4; baseline and differential.
Genevisible; Q9SIC4; AT.
GO; GO:0042644; C:chloroplast nucleoid; IDA:TAIR.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
GO; GO:0019104; F:DNA N-glycosylase activity; IDA:UniProtKB.
GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000703; F:oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity; IBA:GO_Central.
GO; GO:0006284; P:base-excision repair; IDA:UniProtKB.
GO; GO:0006285; P:base-excision repair, AP site formation; IBA:GO_Central.
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; IPR003651; Endonuclease3_FeS-loop_motif.
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.
SMART; SM00525; FES; 1.
SUPFAM; SSF48150; SSF48150; 1.
PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
2: Evidence at transcript level;
4Fe-4S; Alternative splicing; Chloroplast; Complete proteome;
DNA damage; DNA repair; Glycosidase; Hydrolase; Iron; Iron-sulfur;
Lyase; Metal-binding; Plastid; Reference proteome; Transit peptide.
TRANSIT 1 54 Chloroplast. {ECO:0000255}.
CHAIN 55 379 Endonuclease III homolog 1,
chloroplastic.
/FTId=PRO_0000426012.
DOMAIN 244 272 HhH. {ECO:0000255|HAMAP-Rule:MF_03183}.
ACT_SITE 265 265 Nucleophile; for N-glycosylase activity.
{ECO:0000255|HAMAP-Rule:MF_03183}.
METAL 340 340 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
METAL 347 347 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
METAL 350 350 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
METAL 356 356 Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
Rule:MF_03183}.
SITE 284 284 Important for catalytic activity.
{ECO:0000255|HAMAP-Rule:MF_03183}.
VAR_SEQ 54 55 Missing (in isoform 2).
{ECO:0000303|PubMed:14593172}.
/FTId=VSP_053921.
CONFLICT 27 27 S -> I (in Ref. 4; AAM61598).
{ECO:0000305}.
CONFLICT 84 84 Y -> D (in Ref. 4; AAM61598).
{ECO:0000305}.
CONFLICT 132 132 Y -> N (in Ref. 4; AAM61598).
{ECO:0000305}.
CONFLICT 139 139 E -> G (in Ref. 4; AAM61598).
{ECO:0000305}.
CONFLICT 343 343 I -> L (in Ref. 4; AAM61598 and 5;
CAC16135). {ECO:0000305}.
SEQUENCE 379 AA; 41728 MW; 18EF0C9D4DE70A9A CRC64;
MILLVNGGAA TSIHPNAARF YRIGTMSRQI HGAVSSSKHI SLKTQHPLSD SNSELAYGAS
GSETRVYTRK KRLKQEPFEP LEKYSGKGVN THKLCGLPDI EDFAYKKTIG SPSSSRSTET
SITVTSVKTA GYPPENWVEV LEGIRQMRSS EDAPVDSMGC DKAGSFLPPT ERRFAVLLGA
LLSSQTKDQV NNAAIHRLHQ NGLLTPEAVD KADESTIKEL IYPVGFYTRK ATYMKKIARI
CLVKYDGDIP SSLDDLLSLP GIGPKMAHLI LHIAWNDVQG ICVDTHVHRI CNRLGWVSRP
GTKQKTTSPE ETRVALQQWL PKEEWVAINP LLVGFGQMIC TPIRPRCEAC SVSKLCPAAF
KETSSPSSKL KKSNRSKEP


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