END8_ECOLI
ID END8_ECOLI Reviewed; 263 AA.
AC P50465;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 186.
DE RecName: Full=Endonuclease 8;
DE AltName: Full=DNA glycosylase/AP lyase Nei;
DE EC=3.2.2.-;
DE EC=4.2.99.18;
DE AltName: Full=DNA-(apurinic or apyrimidinic site) lyase Nei;
DE AltName: Full=Endonuclease VIII;
GN Name=nei; OrderedLocusNames=b0714, JW0704;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-36; 189-206
RP AND 214-227.
RX PubMed=9171429; DOI=10.1128/jb.179.11.3773-3782.1997;
RA Jiang D., Hatahet Z., Blaisdell J.O., Melamede R.J., Wallace S.S.;
RT "Escherichia coli endonuclease VIII: cloning, sequencing, and
RT overexpression of the nei structural gene and characterization of nei and
RT nei nth mutants.";
RL J. Bacteriol. 179:3773-3782(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9171430; DOI=10.1128/jb.179.11.3783-3785.1997;
RA Saito Y., Uraki F., Nakajima S., Asaeda A., Ono K., Kubo K., Yamamoto K.;
RT "Characterization of endonuclease III (nth) and endonuclease VIII (nei)
RT mutants of Escherichia coli K-12.";
RL J. Bacteriol. 179:3783-3785(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [4]
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 [5]
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 [6]
RP MUTAGENESIS OF PRO-2; GLU-3; GLU-6; ASP-129; ASP-160 AND GLU-174.
RX PubMed=11711552; DOI=10.1074/jbc.m110499200;
RA Burgess S., Jaruga P., Dodson M.L., Dizdaroglu M., Lloyd R.S.;
RT "Determination of active site residues in Escherichia coli endonuclease
RT VIII.";
RL J. Biol. Chem. 277:2938-2944(2002).
RN [7]
RP FUNCTION, AND SUBSTRATES.
RX PubMed=20031487; DOI=10.1016/j.dnarep.2009.11.008;
RA Guo Y., Bandaru V., Jaruga P., Zhao X., Burrows C.J., Iwai S.,
RA Dizdaroglu M., Bond J.P., Wallace S.S.;
RT "The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit
RT different substrate preferences from their Escherichia coli counterparts.";
RL DNA Repair 9:177-190(2010).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.42 ANGSTROMS) IN COMPLEX WITH DNA, AND MUTAGENESIS
RP OF GLU-3; LYS-53; ARG-213 AND ARG-253.
RX PubMed=11847126; DOI=10.1093/emboj/21.4.789;
RA Zharkov D.O., Golan G., Gilboa R., Fernandes A.S., Gerchman S.E.,
RA Kycia J.H., Rieger R.A., Grollman A.P., Shoham G.;
RT "Structural analysis of an Escherichia coli endonuclease VIII covalent
RT reaction intermediate.";
RL EMBO J. 21:789-800(2002).
CC -!- FUNCTION: Involved in base excision repair of DNA damaged by oxidation
CC or by mutagenic agents. Acts as DNA glycosylase that recognizes and
CC removes damaged bases. Has a preference for oxidized pyrimidines, such
CC as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Acts on
CC DNA bubble and 3'-fork structures, suggesting a role in replication-
CC associated DNA repair. Has AP (apurinic/apyrimidinic) lyase activity
CC and introduces nicks in the DNA strand. Cleaves the DNA backbone by
CC beta-delta elimination to generate a single-strand break at the site of
CC the removed base with both 3'- and 5'-phosphates.
CC {ECO:0000269|PubMed:20031487}.
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 -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=Binds 1 zinc ion per subunit.;
CC -!- SIMILARITY: Belongs to the FPG family. {ECO:0000305}.
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DR EMBL; U38616; AAC45355.1; -; Genomic_DNA.
DR EMBL; D89754; BAA20414.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73808.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35378.1; -; Genomic_DNA.
DR PIR; A64807; A64807.
DR RefSeq; NP_415242.1; NC_000913.3.
DR RefSeq; WP_001113989.1; NZ_SSZK01000033.1.
DR PDB; 1K3W; X-ray; 1.42 A; A=2-263.
DR PDB; 1K3X; X-ray; 1.25 A; A=2-263.
DR PDB; 1Q39; X-ray; 2.80 A; A=2-263.
DR PDB; 1Q3B; X-ray; 2.05 A; A=2-263.
DR PDB; 1Q3C; X-ray; 2.30 A; A=2-263.
DR PDB; 2EA0; X-ray; 1.40 A; A=2-263.
DR PDB; 2OPF; X-ray; 1.85 A; A=2-263.
DR PDB; 2OQ4; X-ray; 2.60 A; A/B=2-263.
DR PDB; 6FBU; X-ray; 2.00 A; A=2-263.
DR PDBsum; 1K3W; -.
DR PDBsum; 1K3X; -.
DR PDBsum; 1Q39; -.
DR PDBsum; 1Q3B; -.
DR PDBsum; 1Q3C; -.
DR PDBsum; 2EA0; -.
DR PDBsum; 2OPF; -.
DR PDBsum; 2OQ4; -.
DR PDBsum; 6FBU; -.
DR AlphaFoldDB; P50465; -.
DR SASBDB; P50465; -.
DR SMR; P50465; -.
DR BioGRID; 4259928; 110.
DR DIP; DIP-10327N; -.
DR IntAct; P50465; 13.
DR STRING; 511145.b0714; -.
DR jPOST; P50465; -.
DR PaxDb; P50465; -.
DR PRIDE; P50465; -.
DR EnsemblBacteria; AAC73808; AAC73808; b0714.
DR EnsemblBacteria; BAA35378; BAA35378; BAA35378.
DR GeneID; 945320; -.
DR KEGG; ecj:JW0704; -.
DR KEGG; eco:b0714; -.
DR PATRIC; fig|1411691.4.peg.1559; -.
DR EchoBASE; EB3026; -.
DR eggNOG; COG0266; Bacteria.
DR HOGENOM; CLU_038423_2_2_6; -.
DR InParanoid; P50465; -.
DR OMA; TYWCPRC; -.
DR PhylomeDB; P50465; -.
DR BioCyc; EcoCyc:G6383-MON; -.
DR BioCyc; MetaCyc:G6383-MON; -.
DR BRENDA; 3.2.2.23; 2026.
DR BRENDA; 4.2.99.18; 2026.
DR EvolutionaryTrace; P50465; -.
DR PRO; PR:P50465; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003684; F:damaged DNA binding; IDA:EcoliWiki.
DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:EcoliWiki.
DR GO; GO:0000703; F:oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoliWiki.
DR GO; GO:0006284; P:base-excision repair; IDA:EcoliWiki.
DR CDD; cd08965; EcNei-like_N; 1.
DR Gene3D; 3.20.190.10; -; 1.
DR HAMAP; MF_01253; Endonuclease_8; 1.
DR InterPro; IPR015886; DNA_glyclase/AP_lyase_DNA-bd.
DR InterPro; IPR015887; DNA_glyclase_Znf_dom_DNA_BS.
DR InterPro; IPR044091; EcNei-like_N.
DR InterPro; IPR023713; Endonuclease-VIII.
DR InterPro; IPR012319; FPG_cat.
DR InterPro; IPR035937; MutM-like_N-ter.
DR InterPro; IPR010979; Ribosomal_S13-like_H2TH.
DR InterPro; IPR000214; Znf_DNA_glyclase/AP_lyase.
DR InterPro; IPR010663; Znf_FPG/IleRS.
DR Pfam; PF01149; Fapy_DNA_glyco; 1.
DR Pfam; PF06831; H2TH; 1.
DR Pfam; PF06827; zf-FPG_IleRS; 1.
DR SMART; SM00898; Fapy_DNA_glyco; 1.
DR SMART; SM01232; H2TH; 1.
DR SUPFAM; SSF46946; SSF46946; 1.
DR SUPFAM; SSF81624; SSF81624; 1.
DR PROSITE; PS51068; FPG_CAT; 1.
DR PROSITE; PS01242; ZF_FPG_1; 1.
DR PROSITE; PS51066; ZF_FPG_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA damage; DNA repair;
KW DNA-binding; Glycosidase; Hydrolase; Lyase; Metal-binding;
KW Multifunctional enzyme; Reference proteome; Zinc; Zinc-finger.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9171429"
FT CHAIN 2..263
FT /note="Endonuclease 8"
FT /id="PRO_0000170893"
FT ZN_FING 229..263
FT /note="FPG-type"
FT ACT_SITE 2
FT /note="Schiff-base intermediate with DNA"
FT ACT_SITE 3
FT /note="Proton donor"
FT /evidence="ECO:0000305"
FT ACT_SITE 53
FT /note="Proton donor; for beta-elimination activity"
FT /evidence="ECO:0000305"
FT ACT_SITE 253
FT /note="Proton donor; for delta-elimination activity"
FT /evidence="ECO:0000305"
FT BINDING 70
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000269|PubMed:11847126"
FT BINDING 125
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000269|PubMed:11847126"
FT BINDING 169
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000269|PubMed:11847126"
FT MUTAGEN 2
FT /note="P->T: Loss of glycosylase and AP lyase activity."
FT /evidence="ECO:0000269|PubMed:11711552"
FT MUTAGEN 3
FT /note="E->A,Q: Loss of glycosylase activity. No effect on
FT AP lyase activity."
FT /evidence="ECO:0000269|PubMed:11711552,
FT ECO:0000269|PubMed:11847126"
FT MUTAGEN 3
FT /note="E->D: Much reduced glycosylase activity. No effect
FT on AP lyase activity."
FT /evidence="ECO:0000269|PubMed:11711552,
FT ECO:0000269|PubMed:11847126"
FT MUTAGEN 6
FT /note="E->Q: Reduced glycosylase activity. No effect on AP
FT lyase activity."
FT /evidence="ECO:0000269|PubMed:11711552"
FT MUTAGEN 53
FT /note="K->A: Loss of DNA cleavage at sites containing
FT oxidized pyrimidine. No effect on AP lyase activity."
FT /evidence="ECO:0000269|PubMed:11847126"
FT MUTAGEN 129
FT /note="D->N: Reduced glycosylase activity. No effect on AP
FT lyase activity."
FT /evidence="ECO:0000269|PubMed:11711552"
FT MUTAGEN 160
FT /note="D->N: No effect on glycosylase and AP lyase
FT activity."
FT /evidence="ECO:0000269|PubMed:11711552"
FT MUTAGEN 174
FT /note="E->Q: Loss of glycosylase activity. No effect on AP
FT lyase activity."
FT /evidence="ECO:0000269|PubMed:11711552"
FT MUTAGEN 213
FT /note="R->A: Slightly reduced activity."
FT /evidence="ECO:0000269|PubMed:11847126"
FT MUTAGEN 253
FT /note="R->A: Reduced DNA cleavage at sites containing
FT oxidized pyrimidine. No effect on AP lyase activity."
FT /evidence="ECO:0000269|PubMed:11847126"
FT HELIX 4..18
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 24..30
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 31..35
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 36..40
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 45..51
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 54..59
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 64..68
FT /evidence="ECO:0007829|PDB:1K3X"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 90..95
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 97..105
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 121..125
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 137..145
FT /evidence="ECO:0007829|PDB:1K3X"
FT TURN 147..151
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 154..157
FT /evidence="ECO:0007829|PDB:1K3X"
FT TURN 161..163
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 169..179
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 187..189
FT /evidence="ECO:0007829|PDB:1K3X"
FT HELIX 192..212
FT /evidence="ECO:0007829|PDB:1K3X"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:2OPF"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:1Q3B"
FT STRAND 229..232
FT /evidence="ECO:0007829|PDB:1Q3C"
FT TURN 239..241
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 246..250
FT /evidence="ECO:0007829|PDB:1K3X"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:1K3X"
FT TURN 259..261
FT /evidence="ECO:0007829|PDB:1K3X"
SQ SEQUENCE 263 AA; 29845 MW; 7D10B79F58ADDA24 CRC64;
MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKPYQSQL IGQHVTHVET RGKALLTHFS
NDLTLYSHNQ LYGVWRVVDT GEEPQTTRVL RVKLQTADKT ILLYSASDIE MLTPEQLTTH
PFLQRVGPDV LDPNLTPEVV KERLLSPRFR NRQFAGLLLD QAFLAGLGNY LRVEILWQVG
LTGNHKAKDL NAAQLDALAH ALLEIPRFSY ATRGQVDENK HHGALFRFKV FHRDGEPCER
CGSIIEKTTL SSRPFYWCPG CQH
