ID A0A3B3DJW1_ORYME Unreviewed; 318 AA.
AC A0A3B3DJW1;
DT 05-DEC-2018, integrated into UniProtKB/TrEMBL.
DT 05-DEC-2018, sequence version 1.
DT 27-MAR-2024, entry version 23.
DE RecName: Full=Endonuclease III-like protein 1 {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=NTHL1 {ECO:0000256|HAMAP-Rule:MF_03183,
GN ECO:0000313|Ensembl:ENSOMEP00000029685.1};
OS Oryzias melastigma (Marine medaka).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata;
OC Ovalentaria; Atherinomorphae; Beloniformes; Adrianichthyidae; Oryziinae;
OC Oryzias.
OX NCBI_TaxID=30732 {ECO:0000313|Ensembl:ENSOMEP00000029685.1, ECO:0000313|Proteomes:UP000261560};
RN [1] {ECO:0000313|Ensembl:ENSOMEP00000029685.1}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (SEP-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 -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|HAMAP-Rule:MF_03183}.
CC Mitochondrion {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 AlphaFoldDB; A0A3B3DJW1; -.
DR Ensembl; ENSOMET00000019395.1; ENSOMEP00000029685.1; ENSOMEG00000013509.1.
DR GeneTree; ENSGT00510000047513; -.
DR OMA; WQQFTHL; -.
DR Proteomes; UP000261560; Unplaced.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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: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; 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 SUPFAM; SSF48150; DNA-glycosylase; 1.
DR PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {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};
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|HAMAP-Rule:MF_03183};
KW Iron-sulfur {ECO:0000256|HAMAP-Rule:MF_03183};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_03183};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_03183};
KW Mitochondrion {ECO:0000256|HAMAP-Rule:MF_03183};
KW Nucleus {ECO:0000256|HAMAP-Rule:MF_03183}.
FT DOMAIN 99..249
FT /note="HhH-GPD"
FT /evidence="ECO:0000259|SMART:SM00478"
FT REGION 268..318
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 268..286
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 291..318
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 181
FT /note="Nucleophile; for N-glycosylase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 251
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 258
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
FT BINDING 261
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 SITE 200
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03183"
SQ SEQUENCE 318 AA; 35378 MW; 9C2401813B1358E8 CRC64;
WGSGGAALTA RGCGGTVKRR WGAVSQQPPR LKVEYDNDGS RAIKTERWEP PHWKDQLACI
REMRSRRDAP VDQMGAEKCF DTDAPAHVRR FQVLVSLMLS SQTRDQVTAA AMQKLRAHGC
TAGNILATDD HTLGTLIYPV GFWRNKVKYL KRTAAILQEQ FGGDIPSDVE GLVRLPGVGP
KMAHLAMDIA WNQVSGIGVD THVHRISNRL GWVSKPTKTP EDTRRTLEQW LPRDLWSEIN
WLLVGFGQQM CLPVGPLCSM CLNQHTCPSA HKNSPAKKSH RPTPPSQIKT EPEAAEHKGA
EKDTPVPLPQ RIKVEDET
//
