END3_ECOLI
ID END3_ECOLI Reviewed; 211 AA.
AC P0AB83; P20625;
DT 08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 138.
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};
GN OrderedLocusNames=b1633, JW1625;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, AND FUNCTION.
RX PubMed=2669955; DOI=10.1021/bi00436a048;
RA Asahara H., Wistort P.M., Bank J.F., Bakerian R.H., Cunningham R.P.;
RT "Purification and characterization of Escherichia coli endonuclease III
RT from the cloned nth gene.";
RL Biochemistry 28:4444-4449(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, AND SUBUNIT.
RX PubMed=6371006; DOI=10.1016/s0021-9258(18)91047-1;
RA Breimer L.H., Lindahl T.;
RT "DNA glycosylase activities for thymine residues damaged by ring
RT saturation, fragmentation, or ring contraction are functions of
RT endonuclease III in Escherichia coli.";
RL J. Biol. Chem. 259:5543-5548(1984).
RN [6]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=2449657; DOI=10.1093/nar/16.3.1135;
RA Kim J., Linn S.;
RT "The mechanisms of action of E. coli endonuclease III and T4 UV
RT endonuclease (endonuclease V) at AP sites.";
RL Nucleic Acids Res. 16:1135-1141(1988).
RN [7]
RP COFACTOR.
RX PubMed=8092678; DOI=10.1111/j.1749-6632.1994.tb52818.x;
RA Cunningham R.P., Ahern H., Xing D., Thayer M.M., Tainer J.A.;
RT "Structure and function of Escherichia coli endonuclease III.";
RL Ann. N. Y. Acad. Sci. 726:215-222(1994).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=1411536; DOI=10.1126/science.1411536;
RA Kuo C.-F., McRee D., Fisher C.L., O'Handley S.F., Cunningham R.P.,
RA Tainer J.A.;
RT "Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.";
RL Science 258:434-440(1992).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
RP (4FE-4S), COFACTOR, DNA-BINDING, AND MUTAGENESIS OF LYS-120; ASP-138 AND
RP LYS-191.
RX PubMed=7664751; DOI=10.1002/j.1460-2075.1995.tb00083.x;
RA Thayer M.M., Ahern H., Xing D., Cunningham R.P., Tainer J.A.;
RT "Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal
RT structure.";
RL EMBO J. 14:4108-4120(1995).
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 ECO:0000269|PubMed:2449657, ECO:0000269|PubMed:2669955,
CC ECO:0000269|PubMed:6371006}.
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, ECO:0000269|PubMed:2449657};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00942,
CC ECO:0000269|PubMed:7664751, ECO:0000269|PubMed:8092678};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a
CC role in catalysis, but is probably involved in DNA-binding and proper
CC positioning of the enzyme along the DNA strand. {ECO:0000255|HAMAP-
CC Rule:MF_00942, ECO:0000269|PubMed:7664751, ECO:0000269|PubMed:8092678};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:6371006}.
CC -!- INTERACTION:
CC P0AB83; P0AFG8: aceE; NbExp=3; IntAct=EBI-555213, EBI-542683;
CC -!- SIMILARITY: Belongs to the Nth/MutY family. {ECO:0000255|HAMAP-
CC Rule:MF_00942}.
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DR EMBL; J02857; AAA24227.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74705.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15387.1; -; Genomic_DNA.
DR PIR; A32412; A32412.
DR RefSeq; NP_416150.1; NC_000913.3.
DR RefSeq; WP_001030339.1; NZ_STEB01000003.1.
DR PDB; 2ABK; X-ray; 1.85 A; A=1-211.
DR PDBsum; 2ABK; -.
DR AlphaFoldDB; P0AB83; -.
DR SMR; P0AB83; -.
DR BioGRID; 4262186; 123.
DR DIP; DIP-48071N; -.
DR IntAct; P0AB83; 6.
DR STRING; 511145.b1633; -.
DR jPOST; P0AB83; -.
DR PaxDb; P0AB83; -.
DR PRIDE; P0AB83; -.
DR EnsemblBacteria; AAC74705; AAC74705; b1633.
DR EnsemblBacteria; BAA15387; BAA15387; BAA15387.
DR GeneID; 67415663; -.
DR GeneID; 947122; -.
DR KEGG; ecj:JW1625; -.
DR KEGG; eco:b1633; -.
DR PATRIC; fig|1411691.4.peg.628; -.
DR EchoBASE; EB0656; -.
DR eggNOG; COG0177; Bacteria.
DR HOGENOM; CLU_012862_3_0_6; -.
DR InParanoid; P0AB83; -.
DR OMA; QIIWYGR; -.
DR PhylomeDB; P0AB83; -.
DR BioCyc; EcoCyc:EG10662-MON; -.
DR BioCyc; MetaCyc:EG10662-MON; -.
DR BRENDA; 4.2.99.18; 2026.
DR EvolutionaryTrace; P0AB83; -.
DR PRO; PR:P0AB83; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
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; IBA:GO_Central.
DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000703; F:oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity; IDA:EcoCyc.
DR GO; GO:0004844; F:uracil DNA N-glycosylase activity; IDA:EcoCyc.
DR GO; GO:0006285; P:base-excision repair, AP site formation; IDA:EcoCyc.
DR GO; GO:0097510; P:base-excision repair, AP site formation via deaminated base removal; IDA:EcoCyc.
DR GO; GO:0034644; P:cellular response to UV; IDA:EcoCyc.
DR CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; -; 1.
DR HAMAP; MF_00942; 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; IPR005759; Nth.
DR Pfam; PF10576; EndIII_4Fe-2S; 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; SSF48150; 1.
DR TIGRFAMs; TIGR01083; nth; 1.
DR PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
DR PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Direct protein sequencing; DNA damage; DNA repair;
KW DNA-binding; Glycosidase; Hydrolase; Iron; Iron-sulfur; Lyase;
KW Metal-binding; Reference proteome.
FT CHAIN 1..211
FT /note="Endonuclease III"
FT /id="PRO_0000102210"
FT DOMAIN 108..127
FT /note="HhH"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00942"
FT BINDING 187
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:7664751,
FT ECO:0007744|PDB:2ABK"
FT BINDING 194
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:7664751,
FT ECO:0007744|PDB:2ABK"
FT BINDING 197
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:7664751,
FT ECO:0007744|PDB:2ABK"
FT BINDING 203
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:7664751,
FT ECO:0007744|PDB:2ABK"
FT MUTAGEN 120
FT /note="K->Q: 100000-fold decrease in activity and slight
FT decrease in substrate affinity."
FT /evidence="ECO:0000269|PubMed:7664751"
FT MUTAGEN 138
FT /note="D->N: 100-fold decrease in activity and 4-fold
FT increase in substrate affinity."
FT /evidence="ECO:0000269|PubMed:7664751"
FT MUTAGEN 191
FT /note="K->E: Slight decrease in activity and 130-fold
FT increase in substrate affinity."
FT /evidence="ECO:0000269|PubMed:7664751"
FT HELIX 3..16
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 29..38
FT /evidence="ECO:0007829|PDB:2ABK"
FT TURN 39..41
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 44..54
FT /evidence="ECO:0007829|PDB:2ABK"
FT TURN 55..57
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 61..76
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 82..98
FT /evidence="ECO:0007829|PDB:2ABK"
FT TURN 99..102
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 108..113
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 119..130
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 139..148
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 156..166
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:2ABK"
FT TURN 172..174
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 175..185
FT /evidence="ECO:0007829|PDB:2ABK"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:2ABK"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:2ABK"
SQ SEQUENCE 211 AA; 23562 MW; FF4245823B7F902B CRC64;
MNKAKRLEIL TRLRENNPHP TTELNFSSPF ELLIAVLLSA QATDVSVNKA TAKLYPVANT
PAAMLELGVE GVKTYIKTIG LYNSKAENII KTCRILLEQH NGEVPEDRAA LEALPGVGRK
TANVVLNTAF GWPTIAVDTH IFRVCNRTQF APGKNVEQVE EKLLKVVPAE FKVDCHHWLI
LHGRYTCIAR KPRCGSCIIE DLCEYKEKVD I
