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Flap endonuclease Xni (FEN) (EC 3.1.-.-) (Exonuclease IX) (ExoIX)

 XNI_ECOLI               Reviewed;         251 AA.
P38506; Q2MA36; Q46922;
01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
24-NOV-2009, sequence version 3.
20-JUN-2018, entry version 137.
RecName: Full=Flap endonuclease Xni;
Short=FEN;
EC=3.1.-.-;
AltName: Full=Exonuclease IX;
Short=ExoIX;
Name=ygdG; Synonyms=exo, xni; OrderedLocusNames=b2798, JW5446;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=8385012; DOI=10.1111/j.1432-1033.1993.tb17718.x;
Shao Z., Newman E.B.;
"Sequencing and characterization of the sdaB gene from Escherichia
coli K-12.";
Eur. J. Biochem. 212:777-784(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 193-251.
STRAIN=K12;
PubMed=2664711; DOI=10.1093/nar/17.12.4883;
Lu Z., Lin E.C.C.;
"The nucleotide sequence of Escherichia coli genes for L-fucose
dissimilation.";
Nucleic Acids Res. 17:4883-4884(1989).
[5]
IDENTIFICATION.
PubMed=7996866; DOI=10.1006/jtbi.1994.1202;
Sayers J.R.;
"Computer aided identification of a potential 5'-3' exonuclease gene
encoded by Escherichia coli.";
J. Theor. Biol. 170:415-421(1994).
[6]
IDENTIFICATION.
PubMed=7984428; DOI=10.1093/nar/22.22.4756;
Borodovsky M., Rudd K.E., Koonin E.V.;
"Intrinsic and extrinsic approaches for detecting genes in a bacterial
genome.";
Nucleic Acids Res. 22:4756-4767(1994).
[7]
IDENTIFICATION.
PubMed=8026499; DOI=10.1111/j.1432-1033.1994.tb18938.x;
Shao Z., Lin R.T., Newman E.B.;
"Sequencing and characterization of the sdaC gene and identification
of the sdaCB operon in Escherichia coli K12.";
Eur. J. Biochem. 222:901-907(1994).
[8]
PRELIMINARY CHARACTERIZATION.
PubMed=9592142; DOI=10.1093/nar/26.11.2593;
Shafritz K.M., Sandigursky M., Franklin W.A.;
"Exonuclease IX of Escherichia coli.";
Nucleic Acids Res. 26:2593-2597(1998).
[9]
LACK OF FUNCTION IN RECOMBINATION AND REPAIR PATHWAYS.
PubMed=14599740; DOI=10.1016/S1568-7864(03)00135-6;
Lombardo M.-J., Aponyi I., Ray M.P., Sandigursky M., Franklin W.A.,
Rosenberg S.M.;
"xni-deficient Escherichia coli are proficient for recombination and
multiple pathways of repair.";
DNA Repair 2:1175-1183(2003).
[10]
DISRUPTION PHENOTYPE.
STRAIN=K12 / AB1157;
PubMed=17905985; DOI=10.1128/JB.00653-07;
Fukushima S., Itaya M., Kato H., Ogasawara N., Yoshikawa H.;
"Reassessment of the in vivo functions of DNA polymerase I and RNase H
in bacterial cell growth.";
J. Bacteriol. 189:8575-8583(2007).
[11]
INTERACTION WITH SSB AND H-NS, FUNCTION, AND LACK OF 3'-5' EXONUCLEASE
ACTIVITY.
STRAIN=K12 / XL1-Blue;
PubMed=17567612; DOI=10.1093/nar/gkm396;
Hodskinson M.R.G., Allen L.M., Thomson D.P., Sayers J.R.;
"Molecular interactions of Escherichia coli ExoIX and identification
of its associated 3'-5' exonuclease activity.";
Nucleic Acids Res. 35:4094-4102(2007).
[12]
LACK OF 5'-3' EXONUCLEASE ACTIVITY, FUNCTION, AND DISCUSSION OF
SEQUENCE.
STRAIN=K12 / XL1-Blue;
PubMed=19000038; DOI=10.1042/BJ20081637;
Allen L.M., Hodskinson M.R.G., Sayers J.R.;
"Active site substitutions delineate distinct classes of eubacterial
flap endonuclease.";
Biochem. J. 418:285-292(2009).
[13]
X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
DNA-BINDING, COFACTOR, AND MUTAGENESIS OF LYS-67.
STRAIN=K12 / XL1-Blue;
PubMed=23821668; DOI=10.1093/nar/gkt591;
Anstey-Gilbert C.S., Hemsworth G.R., Flemming C.S., Hodskinson M.R.,
Zhang J., Sedelnikova S.E., Stillman T.J., Sayers J.R., Artymiuk P.J.;
"The structure of Escherichia coli ExoIX--implications for DNA binding
and catalysis in flap endonucleases.";
Nucleic Acids Res. 41:8357-8367(2013).
-!- FUNCTION: Has flap endonuclease activity (PubMed:23821668), but
does not seem to have exonuclease activity (PubMed:17567612 and
PubMed:19000038). During DNA replication, flap endonucleases
cleave the 5'-overhanging flap structure that is generated by
displacement synthesis when DNA polymerase encounters the 5'-end
of a downstream Okazaki fragment. {ECO:0000269|PubMed:17567612,
ECO:0000269|PubMed:19000038, ECO:0000269|PubMed:23821668}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:23821668};
Note=Binds 2 Mg(2+) per subunit. Only one magnesium ion has a
direct interaction with the protein, the other interactions are
indirect. {ECO:0000269|PubMed:23821668};
-!- COFACTOR:
Name=K(+); Xref=ChEBI:CHEBI:29103;
Evidence={ECO:0000269|PubMed:23821668};
Note=Binds 1 K(+) per subunit. The potassium ion strongly
increases the affinity for DNA. {ECO:0000269|PubMed:23821668};
-!- SUBUNIT: Interacts with the DNA-binding proteins SSB and H-NS.
{ECO:0000269|PubMed:17567612}.
-!- DISRUPTION PHENOTYPE: Can be deleted, however double-disruptions
of polA and xni are not viable, suggesting they have a redundant
essential function. {ECO:0000269|PubMed:17905985}.
-!- SIMILARITY: Belongs to the Xni family. {ECO:0000305}.
-!- CAUTION: Was initially reported (PubMed:9592142) as a 3'-5'
exonuclease due to contamination of samples. This protein
possesses no such activity (PubMed:17567612 and PubMed:19000038).
{ECO:0000305|PubMed:9592142}.
-!- SEQUENCE CAUTION:
Sequence=AAB40448.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
Sequence=BAE76870.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
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EMBL; L07763; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; U29581; AAB40448.1; ALT_INIT; Genomic_DNA.
EMBL; U00096; AAC75840.2; -; Genomic_DNA.
EMBL; AP009048; BAE76870.1; ALT_INIT; Genomic_DNA.
EMBL; M27177; -; NOT_ANNOTATED_CDS; Genomic_DNA.
PIR; B65062; B65062.
RefSeq; NP_417278.4; NC_000913.3.
RefSeq; WP_000268232.1; NZ_LN832404.1.
PDB; 3ZD8; X-ray; 2.00 A; A/B=1-251.
PDB; 3ZD9; X-ray; 2.00 A; A=1-251.
PDB; 3ZDA; X-ray; 1.50 A; A=1-251.
PDB; 3ZDB; X-ray; 1.47 A; A=1-251.
PDB; 3ZDC; X-ray; 1.53 A; A=1-251.
PDB; 3ZDD; X-ray; 1.50 A; A=1-251.
PDB; 3ZDE; X-ray; 2.45 A; A=1-251.
PDBsum; 3ZD8; -.
PDBsum; 3ZD9; -.
PDBsum; 3ZDA; -.
PDBsum; 3ZDB; -.
PDBsum; 3ZDC; -.
PDBsum; 3ZDD; -.
PDBsum; 3ZDE; -.
ProteinModelPortal; P38506; -.
SMR; P38506; -.
BioGrid; 4259222; 102.
DIP; DIP-11145N; -.
IntAct; P38506; 3.
STRING; 316385.ECDH10B_2967; -.
PaxDb; P38506; -.
PRIDE; P38506; -.
EnsemblBacteria; AAC75840; AAC75840; b2798.
EnsemblBacteria; BAE76870; BAE76870; BAE76870.
GeneID; 947256; -.
KEGG; ecj:JW5446; -.
KEGG; eco:b2798; -.
PATRIC; fig|1411691.4.peg.3935; -.
EchoBASE; EB2275; -.
EcoGene; EG12372; ygdG.
eggNOG; ENOG4105CIQ; Bacteria.
eggNOG; COG0258; LUCA.
HOGENOM; HOG000040580; -.
InParanoid; P38506; -.
KO; K01146; -.
PhylomeDB; P38506; -.
BioCyc; EcoCyc:EG12372-MONOMER; -.
PRO; PR:P38506; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0017108; F:5'-flap endonuclease activity; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0030955; F:potassium ion binding; IDA:UniProtKB.
GO; GO:0033567; P:DNA replication, Okazaki fragment processing; IDA:UniProtKB.
CDD; cd09898; H3TH_53EXO; 1.
HAMAP; MF_01192; Xni; 1.
InterPro; IPR020046; 5-3_exonucl_a-hlix_arch_N.
InterPro; IPR036279; 5-3_exonuclease_C_sf.
InterPro; IPR002421; 5-3_exonuclease_N.
InterPro; IPR020045; DNA_polI_H3TH.
InterPro; IPR038969; FEN_bact-like.
InterPro; IPR008918; HhH2.
InterPro; IPR029060; PIN-like_dom_sf.
InterPro; IPR022895; Xni.
PANTHER; PTHR42646; PTHR42646; 1.
Pfam; PF01367; 5_3_exonuc; 1.
Pfam; PF02739; 5_3_exonuc_N; 1.
SMART; SM00475; 53EXOc; 1.
SMART; SM00279; HhH2; 1.
SUPFAM; SSF47807; SSF47807; 1.
SUPFAM; SSF88723; SSF88723; 1.
1: Evidence at protein level;
3D-structure; Coiled coil; Complete proteome; DNA-binding;
Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
Potassium; Reference proteome.
CHAIN 1 251 Flap endonuclease Xni.
/FTId=PRO_0000101292.
DOMAIN 160 249 5'-3' exonuclease. {ECO:0000255}.
REGION 184 189 Interaction with DNA.
COILED 198 225 {ECO:0000255}.
METAL 104 104 Magnesium.
METAL 171 171 Potassium; via carbonyl oxygen.
METAL 172 172 Potassium; via carbonyl oxygen.
METAL 180 180 Potassium; via carbonyl oxygen.
METAL 182 182 Potassium; via carbonyl oxygen.
METAL 185 185 Potassium; via carbonyl oxygen.
MUTAGEN 67 67 K->A: Strongly reduces flap endonuclease
activity. {ECO:0000269|PubMed:23821668}.
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


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