ID A0A1U7YCY8_NICSY Unreviewed; 299 AA.
AC A0A1U7YCY8;
DT 10-MAY-2017, integrated into UniProtKB/TrEMBL.
DT 10-MAY-2017, sequence version 1.
DT 27-MAR-2024, entry version 24.
DE RecName: Full=Endonuclease III homolog {ECO:0000256|HAMAP-Rule:MF_03183};
DE EC=3.2.2.- {ECO:0000256|HAMAP-Rule:MF_03183};
DE EC=4.2.99.18 {ECO:0000256|HAMAP-Rule:MF_03183};
DE AltName: Full=Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase {ECO:0000256|HAMAP-Rule:MF_03183};
DE Short=DNA glycosylase/AP lyase {ECO:0000256|HAMAP-Rule:MF_03183};
GN Name=LOC104245831 {ECO:0000313|RefSeq:XP_009799826.1};
GN Synonyms=NTH1 {ECO:0000256|HAMAP-Rule:MF_03183};
OS Nicotiana sylvestris (Wood tobacco) (South American tobacco).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae;
OC Nicotiana.
OX NCBI_TaxID=4096 {ECO:0000313|Proteomes:UP000189701, ECO:0000313|RefSeq:XP_009799826.1};
RN [1] {ECO:0000313|Proteomes:UP000189701}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=23773524; DOI=10.1186/gb-2013-14-6-r60;
RA Sierro N., Battey J.N., Ouadi S., Bovet L., Goepfert S., Bakaher N.,
RA Peitsch M.C., Ivanov N.V.;
RT "Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana
RT tomentosiformis.";
RL Genome Biol. 14:R60.1-R60.17(2013).
RN [2] {ECO:0000313|RefSeq:XP_009799826.1}
RP IDENTIFICATION.
RC TISSUE=Leaf {ECO:0000313|RefSeq:XP_009799826.1};
RG RefSeq;
RL Submitted (NOV-2023) to UniProtKB.
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:0000256|HAMAP-
CC Rule:MF_03183}.
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;
CC Evidence={ECO:0000256|ARBA:ARBA00024490, ECO:0000256|HAMAP-
CC Rule:MF_03183};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|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:0000256|HAMAP-Rule:MF_03183};
CC -!- SIMILARITY: Belongs to the Nth/MutY family.
CC {ECO:0000256|ARBA:ARBA00008343, ECO:0000256|HAMAP-Rule:MF_03183}.
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DR RefSeq; XP_009799826.1; XM_009801524.1.
DR AlphaFoldDB; A0A1U7YCY8; -.
DR GeneID; 104245831; -.
DR OrthoDB; 3377194at2759; -.
DR Proteomes; UP000189701; Unplaced.
DR GO; GO:0005634; C:nucleus; IEA:InterPro.
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:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000703; F:oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006285; P:base-excision repair, AP site formation; IEA:UniProtKB-UniRule.
DR CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal); 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 PANTHER; PTHR43286:SF2; ENDONUCLEASE III HOMOLOG; 1.
DR PANTHER; PTHR43286; ENDONUCLEASE III-LIKE PROTEIN 1; 1.
DR Pfam; PF00633; HHH; 1.
DR Pfam; PF00730; HhH-GPD; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SMART; SM00525; FES; 1.
DR SUPFAM; SSF48150; DNA-glycosylase; 1.
DR PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
DR PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_03183};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_03183};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_03183}; Endonuclease {ECO:0000313|RefSeq:XP_009799826.1};
KW Glycosidase {ECO:0000256|ARBA:ARBA00023295, ECO:0000256|HAMAP-
KW Rule:MF_03183};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_03183};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_03183};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_03183};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_03183};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_03183}; Nuclease {ECO:0000313|RefSeq:XP_009799826.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000189701};
KW Transit peptide {ECO:0000256|ARBA:ARBA00022946}.
FT DOMAIN 102..258
FT /note="HhH-GPD"
FT /evidence="ECO:0000259|SMART:SM00478"
FT ACT_SITE 185
FT /note="Nucleophile; for N-glycosylase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 260
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 267
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 270
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 276
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT SITE 204
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
SQ SEQUENCE 299 AA; 33400 MW; 53D8955401520B9E CRC64;
MSLSLLRHTP YLTSAVPLPI QYFFISLTKM PKTRLSTMRQ DSGAPKFQLK LQPPANWERV
IEGIRRMRSS EHAPVDSIDP DEGVTSLQPK ERRFAVLVGS LLSSQTKGHV THEANQRLLE
NGLLSADSMN KADEVTIKSL IYPVGFYTRK ARHLKQVAKI CVSKYDGDIP GTVDELLLLP
GVGPKIAHLV MIMAWNKVEG ICVDTHVHRV SNRLGWVSQP GKKQGTRSPE ETRVSLQQWL
PKEEWVSINL LLVGFGQTIC TPLRPRCAKC TVSEFCPSAF KEISSPASTS RTLSPKKKH
//
