NTH2_ARATH
ID NTH2_ARATH Reviewed; 386 AA.
AC B9DFZ0; Q94EJ4; Q9MA35;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=Endonuclease III homolog 2, chloroplastic {ECO:0000255|HAMAP-Rule:MF_03183};
DE Short=AtNTH2;
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 2 {ECO:0000255|HAMAP-Rule:MF_03183};
DE Short=DNA glycosylase/AP lyase 2 {ECO:0000255|HAMAP-Rule:MF_03183};
DE Flags: Precursor;
GN Name=NTH2; OrderedLocusNames=At1g05900; ORFNames=T20M3.18;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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).
RC STRAIN=cv. Columbia; TISSUE=Root;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP FUNCTION, 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:19372224}.
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=B9DFZ0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=B9DFZ0-2; Sequence=VSP_053922, VSP_053923;
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=AAF29397.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC009999; AAF29397.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27915.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27916.1; -; Genomic_DNA.
DR EMBL; AF410268; AAK95254.1; -; mRNA.
DR EMBL; AY143860; AAN28799.1; -; mRNA.
DR EMBL; AK316958; BAH19657.1; -; mRNA.
DR PIR; A86194; A86194.
DR RefSeq; NP_563752.1; NM_100471.4. [B9DFZ0-2]
DR RefSeq; NP_973767.1; NM_202038.4. [B9DFZ0-1]
DR AlphaFoldDB; B9DFZ0; -.
DR SMR; B9DFZ0; -.
DR STRING; 3702.AT1G05900.2; -.
DR iPTMnet; B9DFZ0; -.
DR PaxDb; B9DFZ0; -.
DR PRIDE; B9DFZ0; -.
DR ProteomicsDB; 249172; -. [B9DFZ0-1]
DR EnsemblPlants; AT1G05900.1; AT1G05900.1; AT1G05900. [B9DFZ0-2]
DR EnsemblPlants; AT1G05900.2; AT1G05900.2; AT1G05900. [B9DFZ0-1]
DR GeneID; 837100; -.
DR Gramene; AT1G05900.1; AT1G05900.1; AT1G05900. [B9DFZ0-2]
DR Gramene; AT1G05900.2; AT1G05900.2; AT1G05900. [B9DFZ0-1]
DR KEGG; ath:AT1G05900; -.
DR Araport; AT1G05900; -.
DR TAIR; locus:2198738; AT1G05900.
DR eggNOG; KOG1921; Eukaryota.
DR HOGENOM; CLU_012862_4_0_1; -.
DR InParanoid; B9DFZ0; -.
DR OMA; CGTCSIT; -.
DR PhylomeDB; B9DFZ0; -.
DR PRO; PR:B9DFZ0; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; B9DFZ0; baseline and differential.
DR Genevisible; B9DFZ0; 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:TAIR.
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:TAIR.
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; 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; 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..50
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 51..386
FT /note="Endonuclease III homolog 2, chloroplastic"
FT /id="PRO_0000426013"
FT DOMAIN 252..278
FT /note="HhH"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT REGION 44..66
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 272
FT /note="Nucleophile; for N-glycosylase activity"
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 354
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT BINDING 357
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT BINDING 363
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT SITE 291
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03183"
FT VAR_SEQ 312..314
FT /note="KTS -> VLL (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_053922"
FT VAR_SEQ 315..386
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_053923"
SQ SEQUENCE 386 AA; 42415 MW; 814269503D6CF14A CRC64;
MILTGAASTF PIVARVLNAM NRRMYAATTL SSAKSISAES LNLRSDSNSE AAHGASESET
RVSLRKKRIK QDDLEPVKKC SARETKARKD MCGLPDIEDS PYKKTNGTAS SRTRKLNSYI
KSTEASPSAS SIKTAGLGIP PENWEKVLEG IRKMKPSEEA PVNAVECDRT GSFLPPKERR
FYVLIGTLLS SQTKEHITGA AVERLHQNGL LTPEAIDKAD ESTIKELIYP VGFYTRKATN
VKKVAKICLM EYDGDIPRTL EELLSLPGVG PKIAHLVLHV AWNDVQGICV DTHVHRICNR
LGWVSKPGTK QKTSSPEETR VALQQWLPKG EWVAINFLLV GFGQTICTPL RPHCGTCSIT
EICPSAFKET PSTSSKLKKS IKSKKL
