NTH1_ARATH
ID NTH1_ARATH Reviewed; 379 AA.
AC Q9SIC4; Q8LF57; Q8VZT5; Q9FT83;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Endonuclease III homolog 1, chloroplastic {ECO:0000255|HAMAP-Rule:MF_03183};
DE Short=AtNTH1;
DE EC=3.2.2.- {ECO:0000255|HAMAP-Rule:MF_03183};
DE EC=4.2.99.18 {ECO:0000255|HAMAP-Rule:MF_03183};
DE AltName: Full=Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase 1 {ECO:0000255|HAMAP-Rule:MF_03183};
DE Short=DNA glycosylase/AP lyase 1 {ECO:0000255|HAMAP-Rule:MF_03183};
DE Flags: Precursor;
GN Name=NTH1 {ECO:0000255|HAMAP-Rule:MF_03183}; OrderedLocusNames=At2g31450;
GN ORFNames=T28P16.6;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 18-379, FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=11094978; DOI=10.1023/a:1006429114451;
RA Roldan-Arjona T., Garcia-Ortiz M.V., Ruiz-Rubio M., Ariza R.R.;
RT "cDNA cloning, expression and functional characterization of an Arabidopsis
RT thaliana homologue of the Escherichia coli DNA repair enzyme endonuclease
RT III.";
RL Plant Mol. Biol. 44:43-52(2000).
RN [6]
RP DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=19372224; DOI=10.1074/jbc.m109.008342;
RA Gutman B.L., Niyogi K.K.;
RT "Evidence for base excision repair of oxidative DNA damage in chloroplasts
RT of Arabidopsis thaliana.";
RL J. Biol. Chem. 284:17006-17012(2009).
CC -!- FUNCTION: Bifunctional DNA N-glycosylase with associated
CC apurinic/apyrimidinic (AP) lyase function that catalyzes the first step
CC in base excision repair (BER), the primary repair pathway for the
CC repair of oxidative DNA damage. The DNA N-glycosylase activity releases
CC the damaged DNA base from DNA by cleaving the N-glycosidic bond,
CC leaving an AP site. The AP lyase activity cleaves the phosphodiester
CC bond 3' to the AP site by a beta-elimination. Primarily recognizes and
CC repairs oxidative base damage of pyrimidines. {ECO:0000255|HAMAP-
CC Rule:MF_03183, ECO:0000269|PubMed:11094978}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-
CC deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-
CC dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-
CC 2'-deoxyribonucleoside-DNA + H(+); Xref=Rhea:RHEA:66592, Rhea:RHEA-
CC COMP:13180, Rhea:RHEA-COMP:16897, Rhea:RHEA-COMP:17067,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:136412, ChEBI:CHEBI:157695,
CC ChEBI:CHEBI:167181; EC=4.2.99.18; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03183};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03183};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a
CC role in catalysis, but is probably involved in the proper positioning
CC of the enzyme along the DNA strand. {ECO:0000255|HAMAP-Rule:MF_03183};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma, chloroplast nucleoid
CC {ECO:0000269|PubMed:19372224}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9SIC4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SIC4-2; Sequence=VSP_053921;
CC -!- TISSUE SPECIFICITY: Expressed at low levels in roots, stems, leaves and
CC flowers. {ECO:0000269|PubMed:11094978}.
CC -!- DISRUPTION PHENOTYPE: No effect on chloroplastic glycosylase-
CC lyase/endonuclease activity, probably due to function redundancy.
CC {ECO:0000269|PubMed:19372224}.
CC -!- SIMILARITY: Belongs to the Nth/MutY family. {ECO:0000255|HAMAP-
CC Rule:MF_03183}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAC16135.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC007169; AAD26474.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC08549.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC08550.1; -; Genomic_DNA.
DR EMBL; AY063851; AAL36207.1; -; mRNA.
DR EMBL; AY091229; AAM14168.1; -; mRNA.
DR EMBL; AY085041; AAM61598.1; -; mRNA.
DR EMBL; AJ272248; CAC16135.1; ALT_INIT; mRNA.
DR PIR; H84720; H84720.
DR RefSeq; NP_001077988.1; NM_001084519.1. [Q9SIC4-2]
DR RefSeq; NP_565725.1; NM_128702.3. [Q9SIC4-1]
DR AlphaFoldDB; Q9SIC4; -.
DR SMR; Q9SIC4; -.
DR STRING; 3702.AT2G31450.1; -.
DR iPTMnet; Q9SIC4; -.
DR PaxDb; Q9SIC4; -.
DR PRIDE; Q9SIC4; -.
DR ProteomicsDB; 248939; -. [Q9SIC4-1]
DR EnsemblPlants; AT2G31450.1; AT2G31450.1; AT2G31450. [Q9SIC4-1]
DR EnsemblPlants; AT2G31450.2; AT2G31450.2; AT2G31450. [Q9SIC4-2]
DR GeneID; 817703; -.
DR Gramene; AT2G31450.1; AT2G31450.1; AT2G31450. [Q9SIC4-1]
DR Gramene; AT2G31450.2; AT2G31450.2; AT2G31450. [Q9SIC4-2]
DR KEGG; ath:AT2G31450; -.
DR Araport; AT2G31450; -.
DR TAIR; locus:2061345; AT2G31450.
DR eggNOG; KOG1921; Eukaryota.
DR InParanoid; Q9SIC4; -.
DR OMA; HREINHM; -.
DR OrthoDB; 1322642at2759; -.
DR PhylomeDB; Q9SIC4; -.
DR BRENDA; 4.2.99.18; 399.
DR PRO; PR:Q9SIC4; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9SIC4; baseline and differential.
DR Genevisible; Q9SIC4; AT.
DR GO; GO:0042644; C:chloroplast nucleoid; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019104; F:DNA N-glycosylase activity; IDA:UniProtKB.
DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000703; F:oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity; IBA:GO_Central.
DR GO; GO:0006284; P:base-excision repair; IDA:UniProtKB.
DR GO; GO:0006285; P:base-excision repair, AP site formation; IBA:GO_Central.
DR GO; GO:0006296; P:nucleotide-excision repair, DNA incision, 5'-to lesion; IBA:GO_Central.
DR CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; -; 1.
DR HAMAP; MF_03183; Endonuclease_III_Nth; 1.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR004036; Endonuclease-III-like_CS2.
DR InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
DR InterPro; IPR004035; Endouclease-III_FeS-bd_BS.
DR InterPro; IPR003265; HhH-GPD_domain.
DR InterPro; IPR023170; HhH_base_excis_C.
DR InterPro; IPR000445; HhH_motif.
DR InterPro; IPR030841; NTH1.
DR Pfam; PF00633; HHH; 1.
DR Pfam; PF00730; HhH-GPD; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SMART; SM00525; FES; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
DR PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
DR PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; Alternative splicing; Chloroplast; DNA damage; DNA repair;
KW Glycosidase; Hydrolase; Iron; Iron-sulfur; Lyase; Metal-binding; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..54
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 55..379
FT /note="Endonuclease III homolog 1, chloroplastic"
FT /id="PRO_0000426012"
FT DOMAIN 244..272
FT /note="HhH"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT ACT_SITE 265
FT /note="Nucleophile; for N-glycosylase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT BINDING 340
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT BINDING 347
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT BINDING 350
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT BINDING 356
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT SITE 284
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT VAR_SEQ 54..55
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_053921"
FT CONFLICT 27
FT /note="S -> I (in Ref. 4; AAM61598)"
FT /evidence="ECO:0000305"
FT CONFLICT 84
FT /note="Y -> D (in Ref. 4; AAM61598)"
FT /evidence="ECO:0000305"
FT CONFLICT 132
FT /note="Y -> N (in Ref. 4; AAM61598)"
FT /evidence="ECO:0000305"
FT CONFLICT 139
FT /note="E -> G (in Ref. 4; AAM61598)"
FT /evidence="ECO:0000305"
FT CONFLICT 343
FT /note="I -> L (in Ref. 4; AAM61598 and 5; CAC16135)"
FT /evidence="ECO:0000305"
SQ 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
