ID   END3_METJA              Reviewed;         344 AA.
AC   Q58030;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   15-DEC-1998, sequence version 2.
DT   27-MAR-2024, entry version 127.
DE   RecName: Full=Endonuclease III {ECO:0000255|HAMAP-Rule:MF_00942};
DE            EC=4.2.99.18 {ECO:0000255|HAMAP-Rule:MF_00942};
DE   AltName: Full=DNA-(apurinic or apyrimidinic site) lyase {ECO:0000255|HAMAP-Rule:MF_00942};
GN   Name=nth {ECO:0000255|HAMAP-Rule:MF_00942}; OrderedLocusNames=MJ0613;
OS   Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS   10045 / NBRC 100440) (Methanococcus jannaschii).
OC   Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC   Methanocaldococcaceae; Methanocaldococcus.
OX   NCBI_TaxID=243232;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX   PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA   Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA   Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA   Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA   Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA   Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA   Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA   Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA   Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT   "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT   jannaschii.";
RL   Science 273:1058-1073(1996).
CC   -!- FUNCTION: DNA repair enzyme that has both DNA N-glycosylase activity
CC       and AP-lyase activity. The DNA N-glycosylase activity releases various
CC       damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving
CC       an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the
CC       phosphodiester bond 3' to the AP site by a beta-elimination, leaving a
CC       3'-terminal unsaturated sugar and a product with a terminal 5'-
CC       phosphate. {ECO:0000255|HAMAP-Rule:MF_00942}.
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_00942};
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00942};
CC       Note=Binds 1 [4Fe-4S] cluster. {ECO:0000255|HAMAP-Rule:MF_00942};
CC   -!- SIMILARITY: Belongs to the Nth/MutY family. {ECO:0000255|HAMAP-
CC       Rule:MF_00942}.
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DR   EMBL; L77117; AAB98606.1; -; Genomic_DNA.
DR   RefSeq; WP_010870118.1; NC_000909.1.
DR   AlphaFoldDB; Q58030; -.
DR   SMR; Q58030; -.
DR   STRING; 243232.MJ_0613; -.
DR   PaxDb; 243232-MJ_0613; -.
DR   EnsemblBacteria; AAB98606; AAB98606; MJ_0613.
DR   GeneID; 1451479; -.
DR   KEGG; mja:MJ_0613; -.
DR   eggNOG; arCOG00459; Archaea.
DR   HOGENOM; CLU_805637_0_0_2; -.
DR   InParanoid; Q58030; -.
DR   OrthoDB; 84708at2157; -.
DR   PhylomeDB; Q58030; -.
DR   Proteomes; UP000000805; Chromosome.
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:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IBA:GO_Central.
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:0006285; P:base-excision repair, AP site formation; IBA:GO_Central.
DR   CDD; cd00056; ENDO3c; 1.
DR   CDD; cd10441; GIY-YIG_COG1833; 1.
DR   Gene3D; 1.10.1670.10; Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal); 1.
DR   HAMAP; MF_00942; Nth; 1.
DR   InterPro; IPR011257; DNA_glycosylase.
DR   InterPro; IPR002837; DUF123.
DR   InterPro; IPR004036; Endonuclease-III-like_CS2.
DR   InterPro; IPR000305; GIY-YIG_endonuc.
DR   InterPro; IPR003265; HhH-GPD_domain.
DR   InterPro; IPR023170; HhH_base_excis_C.
DR   InterPro; IPR000445; HhH_motif.
DR   InterPro; IPR005759; Nth.
DR   PANTHER; PTHR43286; ENDONUCLEASE III-LIKE PROTEIN 1; 1.
DR   PANTHER; PTHR43286:SF1; ENDONUCLEASE III-LIKE PROTEIN 1; 1.
DR   Pfam; PF01986; DUF123; 1.
DR   Pfam; PF00633; HHH; 1.
DR   Pfam; PF00730; HhH-GPD; 1.
DR   SMART; SM00478; ENDO3c; 1.
DR   SMART; SM00465; GIYc; 1.
DR   SUPFAM; SSF48150; DNA-glycosylase; 1.
DR   PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
DR   PROSITE; PS50164; GIY_YIG; 1.
PE   3: Inferred from homology;
KW   4Fe-4S; DNA damage; DNA repair; DNA-binding; Glycosidase; Hydrolase; Iron;
KW   Iron-sulfur; Lyase; Metal-binding; Reference proteome.
FT   CHAIN           1..344
FT                   /note="Endonuclease III"
FT                   /id="PRO_0000102243"
FT   DOMAIN          105..124
FT                   /note="HhH"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00942"
FT   DOMAIN          229..328
FT                   /note="GIY-YIG"
FT   BINDING         184
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00942"
FT   BINDING         190
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00942"
FT   BINDING         193
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00942"
FT   BINDING         201
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00942"
SQ   SEQUENCE   344 AA;  40568 MW;  BC3BEFE1DE778B85 CRC64;
     MELIEILLKK LNKNAVVTEI AKDKDPFKVL ISTIISARTK DEVTEEVSKK LFKEIKDVDD
     LLNIDEEKLA DLIYPAGFYK NKAKNLKKLA KILKENYNGK VPDSLEELLK LPGVGRKTAN
     LVITLAFNKD GICVDTHVHR ICNRWEIVDT ETPEETEFEL RKKLPKKYWK VINNLLVVFG
     REICSSKSKC DKCFKEIKEK CPYYEKIKHF ENILKKFNFR KVSKNKIPNE KGTYILKIRL
     KEGKKIKFGK TERFFKKGYY FYIGSAFGNS MNLKNRIERH LKDDKKMHWH IDYLLKYGKI
     EEIYITNERV ECEVANEFIK KFDFVENFGC SDCKCKSHLF YLKP
//