EX3_ECOLI
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 03-AUG-2022, entry version 201.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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_STEB01000009.1.
DR PDB; 1AKO; X-ray; 1.70 A; A=1-268.
DR PDBsum; 1AKO; -.
DR AlphaFoldDB; P09030; -.
DR SMR; P09030; -.
DR BioGRID; 4261904; 84.
DR DIP; DIP-11148N; -.
DR IntAct; P09030; 17.
DR STRING; 511145.b1749; -.
DR SWISS-2DPAGE; P09030; -.
DR jPOST; P09030; -.
DR PaxDb; P09030; -.
DR PRIDE; P09030; -.
DR EnsemblBacteria; AAC74819; AAC74819; b1749.
DR EnsemblBacteria; BAA15540; BAA15540; BAA15540.
DR GeneID; 946254; -.
DR KEGG; ecj:JW1738; -.
DR KEGG; eco:b1749; -.
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 PhylomeDB; P09030; -.
DR BioCyc; EcoCyc:EG11073-MON; -.
DR BioCyc; MetaCyc:EG11073-MON; -.
DR BRENDA; 3.1.11.2; 2026.
DR EvolutionaryTrace; P09030; -.
DR PRO; PR:P09030; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0008853; F:exodeoxyribonuclease III activity; IDA:EcoCyc.
DR GO; GO:0004527; F:exonuclease activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:EcoCyc.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR CDD; cd09086; ExoIII-like_AP-endo; 1.
DR Gene3D; 3.60.10.10; -; 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 PANTHER; PTHR43250; PTHR43250; 1.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR SUPFAM; SSF56219; SSF56219; 1.
DR TIGRFAMs; TIGR00633; xth; 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.
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 STRAND 176..179
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
