XNI_ECOLI
ID XNI_ECOLI Reviewed; 251 AA.
AC P38506; Q2MA36; Q46922;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 3.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Flap endonuclease Xni;
DE Short=FEN;
DE EC=3.1.-.-;
DE AltName: Full=Exonuclease IX;
DE Short=ExoIX;
GN Name=ygdG; Synonyms=exo, xni; OrderedLocusNames=b2798, JW5446;
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=8385012; DOI=10.1111/j.1432-1033.1993.tb17718.x;
RA Shao Z., Newman E.B.;
RT "Sequencing and characterization of the sdaB gene from Escherichia coli K-
RT 12.";
RL Eur. J. Biochem. 212:777-784(1993).
RN [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 193-251.
RC STRAIN=K12;
RX PubMed=2664711; DOI=10.1093/nar/17.12.4883;
RA Lu Z., Lin E.C.C.;
RT "The nucleotide sequence of Escherichia coli genes for L-fucose
RT dissimilation.";
RL Nucleic Acids Res. 17:4883-4884(1989).
RN [5]
RP IDENTIFICATION.
RX PubMed=7996866; DOI=10.1006/jtbi.1994.1202;
RA Sayers J.R.;
RT "Computer aided identification of a potential 5'-3' exonuclease gene
RT encoded by Escherichia coli.";
RL J. Theor. Biol. 170:415-421(1994).
RN [6]
RP IDENTIFICATION.
RX PubMed=7984428; DOI=10.1093/nar/22.22.4756;
RA Borodovsky M., Rudd K.E., Koonin E.V.;
RT "Intrinsic and extrinsic approaches for detecting genes in a bacterial
RT genome.";
RL Nucleic Acids Res. 22:4756-4767(1994).
RN [7]
RP IDENTIFICATION.
RX PubMed=8026499; DOI=10.1111/j.1432-1033.1994.tb18938.x;
RA Shao Z., Lin R.T., Newman E.B.;
RT "Sequencing and characterization of the sdaC gene and identification of the
RT sdaCB operon in Escherichia coli K12.";
RL Eur. J. Biochem. 222:901-907(1994).
RN [8]
RP PRELIMINARY CHARACTERIZATION.
RX PubMed=9592142; DOI=10.1093/nar/26.11.2593;
RA Shafritz K.M., Sandigursky M., Franklin W.A.;
RT "Exonuclease IX of Escherichia coli.";
RL Nucleic Acids Res. 26:2593-2597(1998).
RN [9]
RP LACK OF FUNCTION IN RECOMBINATION AND REPAIR PATHWAYS.
RX PubMed=14599740; DOI=10.1016/s1568-7864(03)00135-6;
RA Lombardo M.-J., Aponyi I., Ray M.P., Sandigursky M., Franklin W.A.,
RA Rosenberg S.M.;
RT "xni-deficient Escherichia coli are proficient for recombination and
RT multiple pathways of repair.";
RL DNA Repair 2:1175-1183(2003).
RN [10]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / AB1157;
RX PubMed=17905985; DOI=10.1128/jb.00653-07;
RA Fukushima S., Itaya M., Kato H., Ogasawara N., Yoshikawa H.;
RT "Reassessment of the in vivo functions of DNA polymerase I and RNase H in
RT bacterial cell growth.";
RL J. Bacteriol. 189:8575-8583(2007).
RN [11]
RP INTERACTION WITH SSB AND H-NS, FUNCTION, AND LACK OF 3'-5' EXONUCLEASE
RP ACTIVITY.
RC STRAIN=K12 / XL1-Blue;
RX PubMed=17567612; DOI=10.1093/nar/gkm396;
RA Hodskinson M.R.G., Allen L.M., Thomson D.P., Sayers J.R.;
RT "Molecular interactions of Escherichia coli ExoIX and identification of its
RT associated 3'-5' exonuclease activity.";
RL Nucleic Acids Res. 35:4094-4102(2007).
RN [12]
RP LACK OF 5'-3' EXONUCLEASE ACTIVITY, FUNCTION, AND DISCUSSION OF SEQUENCE.
RC STRAIN=K12 / XL1-Blue;
RX PubMed=19000038; DOI=10.1042/bj20081637;
RA Allen L.M., Hodskinson M.R.G., Sayers J.R.;
RT "Active site substitutions delineate distinct classes of eubacterial flap
RT endonuclease.";
RL Biochem. J. 418:285-292(2009).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP DNA-BINDING, COFACTOR, AND MUTAGENESIS OF LYS-67.
RC STRAIN=K12 / XL1-Blue;
RX PubMed=23821668; DOI=10.1093/nar/gkt591;
RA Anstey-Gilbert C.S., Hemsworth G.R., Flemming C.S., Hodskinson M.R.,
RA Zhang J., Sedelnikova S.E., Stillman T.J., Sayers J.R., Artymiuk P.J.;
RT "The structure of Escherichia coli ExoIX--implications for DNA binding and
RT catalysis in flap endonucleases.";
RL Nucleic Acids Res. 41:8357-8367(2013).
CC -!- FUNCTION: Has flap endonuclease activity (PubMed:23821668), but does
CC not seem to have exonuclease activity (PubMed:17567612 and
CC PubMed:19000038). During DNA replication, flap endonucleases cleave the
CC 5'-overhanging flap structure that is generated by displacement
CC synthesis when DNA polymerase encounters the 5'-end of a downstream
CC Okazaki fragment. {ECO:0000269|PubMed:17567612,
CC ECO:0000269|PubMed:19000038, ECO:0000269|PubMed:23821668}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:23821668};
CC Note=Binds 2 Mg(2+) per subunit. Only one magnesium ion has a direct
CC interaction with the protein, the other interactions are indirect.
CC {ECO:0000269|PubMed:23821668};
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103;
CC Evidence={ECO:0000269|PubMed:23821668};
CC Note=Binds 1 K(+) per subunit. The potassium ion strongly increases the
CC affinity for DNA. {ECO:0000269|PubMed:23821668};
CC -!- SUBUNIT: Interacts with the DNA-binding proteins SSB and H-NS.
CC {ECO:0000269|PubMed:17567612}.
CC -!- DISRUPTION PHENOTYPE: Can be deleted, however double-disruptions of
CC polA and xni are not viable, suggesting they have a redundant essential
CC function. {ECO:0000269|PubMed:17905985}.
CC -!- SIMILARITY: Belongs to the Xni family. {ECO:0000305}.
CC -!- CAUTION: Was initially reported (PubMed:9592142) as a 3'-5' exonuclease
CC due to contamination of samples. This protein possesses no such
CC activity (PubMed:17567612 and PubMed:19000038).
CC {ECO:0000305|PubMed:9592142}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB40448.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAE76870.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; L07763; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U29581; AAB40448.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC75840.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE76870.1; ALT_INIT; Genomic_DNA.
DR EMBL; M27177; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; B65062; B65062.
DR RefSeq; NP_417278.4; NC_000913.3.
DR RefSeq; WP_000268232.1; NZ_SSUV01000026.1.
DR RefSeq; WP_001214598.1; NZ_CP011343.2.
DR PDB; 3ZD8; X-ray; 2.00 A; A/B=1-251.
DR PDB; 3ZD9; X-ray; 2.00 A; A=1-251.
DR PDB; 3ZDA; X-ray; 1.50 A; A=1-251.
DR PDB; 3ZDB; X-ray; 1.47 A; A=1-251.
DR PDB; 3ZDC; X-ray; 1.53 A; A=1-251.
DR PDB; 3ZDD; X-ray; 1.50 A; A=1-251.
DR PDB; 3ZDE; X-ray; 2.45 A; A=1-251.
DR PDBsum; 3ZD8; -.
DR PDBsum; 3ZD9; -.
DR PDBsum; 3ZDA; -.
DR PDBsum; 3ZDB; -.
DR PDBsum; 3ZDC; -.
DR PDBsum; 3ZDD; -.
DR PDBsum; 3ZDE; -.
DR AlphaFoldDB; P38506; -.
DR SMR; P38506; -.
DR BioGRID; 4259222; 102.
DR BioGRID; 851586; 1.
DR DIP; DIP-11145N; -.
DR IntAct; P38506; 3.
DR STRING; 511145.b2798; -.
DR jPOST; P38506; -.
DR PaxDb; P38506; -.
DR PRIDE; P38506; -.
DR EnsemblBacteria; AAC75840; AAC75840; b2798.
DR EnsemblBacteria; BAE76870; BAE76870; BAE76870.
DR GeneID; 947256; -.
DR KEGG; ecj:JW5446; -.
DR KEGG; eco:b2798; -.
DR PATRIC; fig|1411691.4.peg.3935; -.
DR EchoBASE; EB2275; -.
DR eggNOG; COG0258; Bacteria.
DR HOGENOM; CLU_004675_1_2_6; -.
DR InParanoid; P38506; -.
DR OMA; WRVDLIP; -.
DR PhylomeDB; P38506; -.
DR BioCyc; EcoCyc:EG12372-MON; -.
DR PRO; PR:P38506; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0017108; F:5'-flap endonuclease activity; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030955; F:potassium ion binding; IDA:UniProtKB.
DR GO; GO:0033567; P:DNA replication, Okazaki fragment processing; IDA:UniProtKB.
DR CDD; cd09898; H3TH_53EXO; 1.
DR HAMAP; MF_01192; Xni; 1.
DR InterPro; IPR020046; 5-3_exonucl_a-hlix_arch_N.
DR InterPro; IPR002421; 5-3_exonuclease.
DR InterPro; IPR036279; 5-3_exonuclease_C_sf.
DR InterPro; IPR020045; DNA_polI_H3TH.
DR InterPro; IPR038969; FEN.
DR InterPro; IPR008918; HhH2.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR022895; Xni.
DR PANTHER; PTHR42646; PTHR42646; 1.
DR Pfam; PF01367; 5_3_exonuc; 1.
DR Pfam; PF02739; 5_3_exonuc_N; 1.
DR SMART; SM00475; 53EXOc; 1.
DR SMART; SM00279; HhH2; 1.
DR SUPFAM; SSF47807; SSF47807; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; DNA-binding; Endonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Potassium; Reference proteome.
FT CHAIN 1..251
FT /note="Flap endonuclease Xni"
FT /id="PRO_0000101292"
FT DOMAIN 160..249
FT /note="5'-3' exonuclease"
FT /evidence="ECO:0000255"
FT REGION 184..189
FT /note="Interaction with DNA"
FT COILED 198..225
FT /evidence="ECO:0000255"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 171
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 172
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 180
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 182
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 185
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT MUTAGEN 67
FT /note="K->A: Strongly reduces flap endonuclease activity."
FT /evidence="ECO:0000269|PubMed:23821668"
SQ SEQUENCE 251 AA; 28166 MW; 937A2CDCC58B03A5 CRC64;
MAVHLLIVDA LNLIRRIHAV QGSPCVETCQ HALDQLIMHS QPTHAVAVFD DENRSSGWRH
QRLPDYKAGR PPMPEELHDE MPALRAAFEQ RGVPCWSTSG NEADDLAATL AVKVTQAGHQ
ATIVSTDKGY CQLLSPTLRI RDYFQKRWLD APFIDKEFGV QPQQLPDYWG LAGISSSKVP
GVAGIGPKSA TQLLVEFQSL EGIYENLDAV AEKWRKKLET HKEMAFLCRD IARLQTDLHI
DGNLQQLRLV R
