ID   EX3_ECOLI               Reviewed;         268 AA.
AC   P09030;
DT   01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 4.
DT   02-SEP-2026, entry version 217.
DE   RecName: Full=Exodeoxyribonuclease III;
DE            Short=EXO III;
DE            Short=Exonuclease III;
DE            EC=3.1.11.2;
DE   AltName: Full=AP endonuclease VI;
GN   Name=xthA; Synonyms=xth; OrderedLocusNames=b1749, JW1738;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=3049539; DOI=10.1128/jb.170.10.4542-4547.1988;
RA   Saporito S.M., Smith-White B.J., Cunningham R.P.;
RT   "Nucleotide sequence of the xth gene of Escherichia coli K-12.";
RL   J. Bacteriol. 170:4542-4547(1988).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RA   Wurst H., Hoheisel J.D., Pohl F.M.;
RL   Submitted (NOV-1988) to the EMBL/GenBank/DDBJ databases.
RN   [3]
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   [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   CHARACTERIZATION.
RX   PubMed=8948651; DOI=10.1093/nar/24.22.4572;
RA   Shida T., Noda M., Sekiguchi J.;
RT   "Cleavage of single- and double-stranded DNAs containing an abasic residue
RT   by Escherichia coli exonuclease III (AP endonuclease VI).";
RL   Nucleic Acids Res. 24:4572-4576(1996).
RN   [7]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), AND COFACTOR.
RX   PubMed=7885481; DOI=10.1038/374381a0;
RA   Mol C.D., Kuo C.-F., Thayer M.M., Cunningham R.P., Tainer J.A.;
RT   "Structure and function of the multifunctional DNA-repair enzyme
RT   exonuclease III.";
RL   Nature 374:381-386(1995).
CC   -!- FUNCTION: Major apurinic-apyrimidinic endonuclease of E.coli. It
CC       removes the damaged DNA at cytosines and guanines by cleaving on the
CC       3'-side of the AP site by a beta-elimination reaction. It exhibits 3'-
CC       5'-exonuclease, 3'-phosphomonoesterase, 3'-repair diesterase and
CC       ribonuclease H activities.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC         nucleoside 5'-phosphates.; EC=3.1.11.2;
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Probably binds two magnesium or manganese ions per subunit.
CC       {ECO:0000250};
CC   -!- SUBUNIT: Monomer.
CC   -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC       {ECO:0000305}.
CC   -!- WEB RESOURCE: Name=Wikipedia; Note=Exonuclease III entry;
CC       URL="https://en.wikipedia.org/wiki/Exonuclease_III";
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DR   EMBL; X13002; CAA31424.1; -; Genomic_DNA.
DR   EMBL; M22592; AAA24767.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC74819.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA15540.1; -; Genomic_DNA.
DR   PIR; E64934; NCECX3.
DR   RefSeq; NP_416263.1; NC_000913.3.
DR   RefSeq; WP_000673918.1; NZ_CP009789.1.
DR   PDB; 1AKO; X-ray; 1.70 A; A=1-268.
DR   AlphaFoldDB; P09030; -.
DR   MDposit; P09030; -.
DR   SMR; P09030; -.
DR   BioGRID; 4261904; 96.
DR   DIP; DIP-11148N; -.
DR   FunCoup; P09030; 728.
DR   IntAct; P09030; 17.
DR   STRING; 511145.b1749; -.
DR   jPOST; P09030; -.
DR   PaxDb; 511145-b1749; -.
DR   EnsemblBacteria; AAC74819; AAC74819; b1749.
DR   GeneID; 93775963; -.
DR   GeneID; 946254; -.
DR   KEGG; ecj:JW1738; -.
DR   KEGG; eco:b1749; -.
DR   KEGG; ecoc:C3026_09990; -.
DR   PATRIC; fig|1411691.4.peg.506; -.
DR   EchoBASE; EB1066; -.
DR   eggNOG; COG0708; Bacteria.
DR   HOGENOM; CLU_027539_0_3_6; -.
DR   InParanoid; P09030; -.
DR   OMA; WWSYRGR; -.
DR   OrthoDB; 9803914at2; -.
DR   PhylomeDB; P09030; -.
DR   BioCyc; EcoCyc:EG11073-MONOMER; -.
DR   BioCyc; MetaCyc:EG11073-MONOMER; -.
DR   BRENDA; 3.1.11.2; 2026.
DR   EvolutionaryTrace; P09030; -.
DR   PRO; PR:P09030; -.
DR   Proteomes; UP000000625; Chromosome.
DR   AbasyAtlas; P09030; -.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0008311; F:double-stranded DNA 3'-5' DNA exonuclease activity; IDA:EcoCyc.
DR   GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR   GO; GO:0004527; F:exonuclease activity; IDA:EcoCyc.
DR   GO; GO:0006974; P:DNA damage response; IDA:EcoCyc.
DR   GO; GO:0006281; P:DNA repair; IEA:InterPro.
DR   CDD; cd09086; ExoIII-like_AP-endo; 1.
DR   FunFam; 3.60.10.10:FF:000006; Exodeoxyribonuclease III; 1.
DR   Gene3D; 3.60.10.10; Endonuclease/exonuclease/phosphatase; 1.
DR   InterPro; IPR004808; AP_endonuc_1.
DR   InterPro; IPR020847; AP_endonuclease_F1_BS.
DR   InterPro; IPR020848; AP_endonuclease_F1_CS.
DR   InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR   InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR   InterPro; IPR037493; ExoIII-like.
DR   NCBIfam; TIGR00195; exoDNase_III; 1.
DR   NCBIfam; NF008733; PRK11756.1; 1.
DR   NCBIfam; TIGR00633; xth; 1.
DR   PANTHER; PTHR43250; EXODEOXYRIBONUCLEASE III; 1.
DR   PANTHER; PTHR43250:SF2; EXODEOXYRIBONUCLEASE III; 1.
DR   Pfam; PF03372; Exo_endo_phos; 1.
DR   SUPFAM; SSF56219; DNase I-like; 1.
DR   PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
DR   PROSITE; PS00727; AP_NUCLEASE_F1_2; 1.
DR   PROSITE; PS00728; AP_NUCLEASE_F1_3; 1.
DR   PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
DR   PDBsum; 1AKO; -.
PE   1: Evidence at protein level;
KW   3D-structure; DNA damage; DNA repair; Exonuclease; Hydrolase; Magnesium;
KW   Metal-binding; Nuclease; Reference proteome.
FT   CHAIN           1..268
FT                   /note="Exodeoxyribonuclease III"
FT                   /id="PRO_0000200021"
FT   ACT_SITE        109
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        151
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         34
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         151
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         153
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         258
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   SITE            153
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250"
FT   SITE            229
FT                   /note="Important for catalytic activity"
FT                   /evidence="ECO:0000250"
FT   SITE            259
FT                   /note="Interaction with DNA substrate"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        49..50
FT                   /note="KL -> NV (in Ref. 1; AAA24767)"
FT                   /evidence="ECO:0000305"
FT   STRAND          2..7
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           11..13
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           15..25
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          28..33
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           39..41
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           44..49
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          53..59
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          62..71
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          74..80
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           85..88
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          91..98
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          101..109
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           121..139
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          146..151
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           158..160
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           165..174
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           181..192
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          195..197
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           198..202
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   TURN            215..218
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           219..222
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          229..234
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           235..238
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          241..246
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   HELIX           248..251
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          253..255
FT                   /evidence="ECO:0007829|PDB:1AKO"
FT   STRAND          262..266
FT                   /evidence="ECO:0007829|PDB:1AKO"
SQ   SEQUENCE   268 AA;  30969 MW;  09E0E263DCF38634 CRC64;
     MKFVSFNING LRARPHQLEA IVEKHQPDVI GLQETKVHDD MFPLEEVAKL GYNVFYHGQK
     GHYGVALLTK ETPIAVRRGF PGDDEEAQRR IIMAEIPSLL GNVTVINGYF PQGESRDHPI
     KFPAKAQFYQ NLQNYLETEL KRDNPVLIMG DMNISPTDLD IGIGEENRKR WLRTGKCSFL
     PEEREWMDRL MSWGLVDTFR HANPQTADRF SWFDYRSKGF DDNRGLRIDL LLASQPLAEC
     CVETGIDYEI RSMEKPSDHA PVWATFRR
//