ID A0A1S3VUD5_VIGRR Unreviewed; 322 AA.
AC A0A1S3VUD5;
DT 12-APR-2017, integrated into UniProtKB/TrEMBL.
DT 12-APR-2017, sequence version 1.
DT 27-MAR-2024, entry version 28.
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=LOC106778461 {ECO:0000313|RefSeq:XP_014521910.1};
GN Synonyms=NTH1 {ECO:0000256|HAMAP-Rule:MF_03183};
OS Vigna radiata var. radiata (Mung bean) (Phaseolus aureus).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Vigna.
OX NCBI_TaxID=3916 {ECO:0000313|Proteomes:UP000087766, ECO:0000313|RefSeq:XP_014521910.1};
RN [1] {ECO:0000313|RefSeq:XP_014521910.1}
RP IDENTIFICATION.
RC TISSUE=Leaf {ECO:0000313|RefSeq:XP_014521910.1};
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_014521910.1; XM_014666424.2.
DR AlphaFoldDB; A0A1S3VUD5; -.
DR GeneID; 106778461; -.
DR KEGG; vra:106778461; -.
DR OrthoDB; 3377194at2759; -.
DR Proteomes; UP000087766; 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; IPR003265; HhH-GPD_domain.
DR InterPro; IPR023170; HhH_base_excis_C.
DR InterPro; IPR000445; HhH_motif.
DR InterPro; IPR030841; NTH1.
DR PANTHER; PTHR43286; ENDONUCLEASE III-LIKE PROTEIN 1; 1.
DR PANTHER; PTHR43286:SF1; 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; 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_014521910.1};
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_014521910.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000087766};
KW Transit peptide {ECO:0000256|ARBA:ARBA00022946}.
FT DOMAIN 125..281
FT /note="HhH-GPD"
FT /evidence="ECO:0000259|SMART:SM00478"
FT ACT_SITE 208
FT /note="Nucleophile; for N-glycosylase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 283
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 290
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 293
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 299
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT SITE 227
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
SQ SEQUENCE 322 AA; 35757 MW; 0B25AB60999A1A09 CRC64;
MLGRIHVSIP AKTTQLFSSK PHPVSQLRAS VTTKTTRKSL QLQHVPEIET ENHQKGIAGF
ALARARSNES VQSGEAPANW EKVLQGIRQM RSSADEHEPV AHEETADNTV LPKERRFAVL
ASSILSSQTK GHVSRGAAQC LHENGLLTAE AMNKADEETI KKLIYPVGFY TRKASYLKKV
ANICLMKYDG DIPSSIEELL LLPGVGPKIA HLVMIRGWNN VQGICVDTHV HRICNRLGWV
LRSGSKEKTL TPEETRQRLQ LWLPKEEWVP INPLLVGFGR SICTPLRPHC GECSVSSFCP
SAYKEASSFS SKSRKITLNK KP
//
