END4_ECOLI
ID END4_ECOLI Reviewed; 285 AA.
AC P0A6C1; P12638; P78086; Q2MAS0;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=Endonuclease 4;
DE EC=3.1.21.2;
DE AltName: Full=Endodeoxyribonuclease IV;
DE AltName: Full=Endonuclease IV;
GN Name=nfo; OrderedLocusNames=b2159, JW2146;
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=2460435; DOI=10.1128/jb.170.11.5141-5145.1988;
RA Saporito S.M., Cunningham R.P.;
RT "Nucleotide sequence of the nfo gene of Escherichia coli K-12.";
RL J. Bacteriol. 170:5141-5145(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / BHB2600;
RA Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
RA Church G.M.;
RT "Automated multiplex sequencing of the E.coli genome.";
RL Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
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 METAL-BINDING STUDIES.
RX PubMed=1720775; DOI=10.1016/s0021-9258(18)54438-0;
RA Levin J.D., Shapiro R., Demple B.;
RT "Metalloenzymes in DNA repair. Escherichia coli endonuclease IV and
RT Saccharomyces cerevisiae Apn1.";
RL J. Biol. Chem. 266:22893-22898(1991).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.02 ANGSTROMS).
RX PubMed=10458614; DOI=10.1016/s0092-8674(00)81968-6;
RA Hosfield D.J., Guan Y., Haas B.J., Cunningham R.P., Tainer J.A.;
RT "Structure of the DNA repair enzyme endonuclease IV and its DNA complex:
RT double-nucleotide flipping at abasic sites and three-metal-ion catalysis.";
RL Cell 98:397-408(1999).
CC -!- FUNCTION: Endonuclease IV plays a role in DNA repair. It cleaves
CC phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating
CC a 3'-hydroxyl group and a 5'-terminal sugar phosphate. It
CC preferentially attacks modified AP sites created by bleomycin and
CC neocarzinostatin.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphooligonucleotide end-
CC products.; EC=3.1.21.2;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Note=Binds 3 Zn(2+) ions. Can also bind Mn(2+) ions.;
CC -!- SUBUNIT: Monomer.
CC -!- INDUCTION: Endonuclease IV is induced by agents which generate
CC superoxide radical anions.
CC -!- SIMILARITY: Belongs to the AP endonuclease 2 family.
CC {ECO:0000255|HAMAP-Rule:MF_00152, ECO:0000305}.
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DR EMBL; M22591; AAA24216.1; -; Genomic_DNA.
DR EMBL; U00007; AAA60529.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75220.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76636.1; -; Genomic_DNA.
DR PIR; F64984; NDEC4.
DR RefSeq; NP_416664.1; NC_000913.3.
DR RefSeq; WP_000873894.1; NZ_LN832404.1.
DR PDB; 1QTW; X-ray; 1.02 A; A=1-285.
DR PDB; 1QUM; X-ray; 1.55 A; A=1-285.
DR PDB; 2NQ9; X-ray; 1.45 A; A=1-285.
DR PDB; 2NQH; X-ray; 1.10 A; A=1-285.
DR PDB; 2NQJ; X-ray; 2.45 A; A/B=1-285.
DR PDB; 4K1G; X-ray; 1.90 A; A/B=1-285.
DR PDBsum; 1QTW; -.
DR PDBsum; 1QUM; -.
DR PDBsum; 2NQ9; -.
DR PDBsum; 2NQH; -.
DR PDBsum; 2NQJ; -.
DR PDBsum; 4K1G; -.
DR AlphaFoldDB; P0A6C1; -.
DR SMR; P0A6C1; -.
DR BioGRID; 4261799; 26.
DR DIP; DIP-47966N; -.
DR IntAct; P0A6C1; 10.
DR STRING; 511145.b2159; -.
DR ChEMBL; CHEMBL1293285; -.
DR jPOST; P0A6C1; -.
DR PaxDb; P0A6C1; -.
DR PRIDE; P0A6C1; -.
DR EnsemblBacteria; AAC75220; AAC75220; b2159.
DR EnsemblBacteria; BAE76636; BAE76636; BAE76636.
DR GeneID; 946669; -.
DR KEGG; ecj:JW2146; -.
DR KEGG; eco:b2159; -.
DR PATRIC; fig|1411691.4.peg.80; -.
DR EchoBASE; EB0645; -.
DR eggNOG; COG0648; Bacteria.
DR HOGENOM; CLU_025885_0_4_6; -.
DR InParanoid; P0A6C1; -.
DR OMA; HPGSHLK; -.
DR PhylomeDB; P0A6C1; -.
DR BioCyc; EcoCyc:EG10651-MON; -.
DR BioCyc; MetaCyc:EG10651-MON; -.
DR BRENDA; 3.1.21.2; 2026.
DR EvolutionaryTrace; P0A6C1; -.
DR PRO; PR:P0A6C1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008296; F:3'-5'-exodeoxyribonuclease activity; IDA:EcoCyc.
DR GO; GO:0008833; F:deoxyribonuclease IV (phage-T4-induced) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:EcoCyc.
DR GO; GO:0004519; F:endonuclease activity; IDA:EcoCyc.
DR GO; GO:0016791; F:phosphatase activity; IDA:EcoCyc.
DR GO; GO:0008081; F:phosphoric diester hydrolase activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
DR GO; GO:0006281; P:DNA repair; IMP:EcoCyc.
DR CDD; cd00019; AP2Ec; 1.
DR HAMAP; MF_00152; Nfo; 1.
DR InterPro; IPR001719; AP_endonuc_2.
DR InterPro; IPR018246; AP_endonuc_F2_Zn_BS.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR PANTHER; PTHR21445; PTHR21445; 1.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR SMART; SM00518; AP2Ec; 1.
DR SUPFAM; SSF51658; SSF51658; 1.
DR TIGRFAMs; TIGR00587; nfo; 1.
DR PROSITE; PS00729; AP_NUCLEASE_F2_1; 1.
DR PROSITE; PS00730; AP_NUCLEASE_F2_2; 1.
DR PROSITE; PS00731; AP_NUCLEASE_F2_3; 1.
DR PROSITE; PS51432; AP_NUCLEASE_F2_4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; Endonuclease; Hydrolase; Manganese;
KW Metal-binding; Nuclease; Reference proteome; Zinc.
FT CHAIN 1..285
FT /note="Endonuclease 4"
FT /id="PRO_0000190838"
FT BINDING 69
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 145
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 145
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 179
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 182
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT BINDING 216
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 229
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT BINDING 231
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT BINDING 261
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT CONFLICT 10
FT /note="A -> R (in Ref. 1; AAA24216)"
FT /evidence="ECO:0000305"
FT CONFLICT 273
FT /note="A -> T (in Ref. 2; AAA60529)"
FT /evidence="ECO:0000305"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 14..23
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:4K1G"
FT HELIX 46..58
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 66..69
FT /evidence="ECO:0007829|PDB:1QUM"
FT HELIX 81..100
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 105..108
FT /evidence="ECO:0007829|PDB:1QTW"
FT TURN 114..116
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 119..136
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 158..167
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 171..173
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 174..179
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 180..186
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 193..206
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 212..217
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 219..222
FT /evidence="ECO:0007829|PDB:1QTW"
FT TURN 234..236
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 242..248
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 251..253
FT /evidence="ECO:0007829|PDB:1QTW"
FT STRAND 256..260
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:1QTW"
FT HELIX 268..278
FT /evidence="ECO:0007829|PDB:1QTW"
SQ SEQUENCE 285 AA; 31480 MW; EAAE5861E54C47FD CRC64;
MKYIGAHVSA AGGLANAAIR AAEIDATAFA LFTKNQRQWR AAPLTTQTID EFKAACEKYH
YTSAQILPHD SYLINLGHPV TEALEKSRDA FIDEMQRCEQ LGLSLLNFHP GSHLMQISEE
DCLARIAESI NIALDKTQGV TAVIENTAGQ GSNLGFKFEH LAAIIDGVED KSRVGVCIDT
CHAFAAGYDL RTPAECEKTF ADFARTVGFK YLRGMHLNDA KSTFGSRVDR HHSLGEGNIG
HDAFRWIMQD DRFDGIPLIL ETINPDIWAE EIAWLKAQQT EKAVA
