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Flap endonuclease 1 (FEN-1) (EC 3.1.-.-) (Flap structure-specific endonuclease 1)

 F9WFI3_TRYCI            Unreviewed;       492 AA.
F9WFI3;
19-OCT-2011, integrated into UniProtKB/TrEMBL.
19-OCT-2011, sequence version 1.
05-DEC-2018, entry version 46.
RecName: Full=Flap endonuclease 1 {ECO:0000256|HAMAP-Rule:MF_03140};
Short=FEN-1 {ECO:0000256|HAMAP-Rule:MF_03140};
EC=3.1.-.- {ECO:0000256|HAMAP-Rule:MF_03140};
AltName: Full=Flap structure-specific endonuclease 1 {ECO:0000256|HAMAP-Rule:MF_03140};
Name=FEN1 {ECO:0000256|HAMAP-Rule:MF_03140};
ORFNames=TCIL3000_0_10230 {ECO:0000313|EMBL:CCD16055.1};
Trypanosoma congolense (strain IL3000).
Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma;
Nannomonas.
NCBI_TaxID=1068625 {ECO:0000313|EMBL:CCD16055.1, ECO:0000313|Proteomes:UP000000702};
[1] {ECO:0000313|Proteomes:UP000000702}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=IL3000 {ECO:0000313|Proteomes:UP000000702};
Jackson A.P., Berry A., Allison H.C., Burton P., Anderson J.,
Aslett M., Brown R., Corton N., Harris D., Hauser H., Gamble J.,
Gilderthorp R., McQuillan J., Quail M.A., Sanders M., van Tonder A.,
Ginger M.L., Donelson J.E., Field M.C., Barry J.D., Berriman M.,
Hertz-Fowler C.;
"Divergent evolution of antigenic variation in African trypanosomes.";
Submitted (JUL-2011) to the EMBL/GenBank/DDBJ databases.
[2] {ECO:0000313|Proteomes:UP000000702}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=IL3000 {ECO:0000313|Proteomes:UP000000702};
Jackson A.P., Berry A., Allison H.C., Burton P., Anderson J.,
Aslett M., Brown R., Corton N., Harris D., Hauser H., Gamble J.,
Gilderthorp R., McQuillan J., Quail M.A., Sanders M., Van Tonder A.,
Ginger M.L., Donelson J.E., Field M.C., Barry J.D., Berriman M.,
Hertz-Fowler C.;
"Divergent evolution of antigenic variation in African trypanosomes.";
Submitted (JUL-2011) to the EMBL/GenBank/DDBJ databases.
[3] {ECO:0000313|EMBL:CCD16055.1, ECO:0000313|Proteomes:UP000000702}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=IL3000 {ECO:0000313|EMBL:CCD16055.1,
ECO:0000313|Proteomes:UP000000702};
PubMed=22331916; DOI=10.1073/pnas.1117313109;
Jackson A.P., Berry A., Aslett M., Allison H.C., Burton P.,
Vavrova-Anderson J., Brown R., Browne H., Corton N., Hauser H.,
Gamble J., Gilderthorp R., Marcello L., McQuillan J., Otto T.D.,
Quail M.A., Sanders M.J., van Tonder A., Ginger M.L., Field M.C.,
Barry J.D., Hertz-Fowler C., Berriman M.;
"Antigenic diversity is generated by distinct evolutionary mechanisms
in African trypanosome species.";
Proc. Natl. Acad. Sci. U.S.A. 109:3416-3421(2012).
-!- FUNCTION: Structure-specific nuclease with 5'-flap endonuclease
and 5'-3' exonuclease activities involved in DNA replication and
repair. During DNA replication, cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis when DNA
polymerase encounters the 5'-end of a downstream Okazaki fragment.
It enters the flap from the 5'-end and then tracks to cleave the
flap base, leaving a nick for ligation. Also involved in the long
patch base excision repair (LP-BER) pathway, by cleaving within
the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a
genome stabilization factor that prevents flaps from equilibrating
into structurs that lead to duplications and deletions. Also
possesses 5'-3' exonuclease activity on nicked or gapped double-
stranded DNA, and exhibits RNase H activity. Also involved in
replication and repair of rDNA and in repairing mitochondrial DNA.
{ECO:0000256|HAMAP-Rule:MF_03140, ECO:0000256|SAAS:SAAS00882638}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000256|HAMAP-Rule:MF_03140};
Note=Binds 2 magnesium ions per subunit. They probably participate
in the reaction catalyzed by the enzyme. May bind an additional
third magnesium ion after substrate binding. {ECO:0000256|HAMAP-
Rule:MF_03140};
-!- SUBUNIT: Interacts with PCNA. Three molecules of FEN1 bind to one
PCNA trimer with each molecule binding to one PCNA monomer. PCNA
stimulates the nuclease activity without altering cleavage
specificity. {ECO:0000256|HAMAP-Rule:MF_03140}.
-!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000256|HAMAP-
Rule:MF_03140, ECO:0000256|SAAS:SAAS00882753}. Nucleus, nucleolus
{ECO:0000256|HAMAP-Rule:MF_03140}. Nucleus, nucleoplasm
{ECO:0000256|HAMAP-Rule:MF_03140}. Note=Resides mostly in the
nucleoli and relocalizes to the nucleoplasm upon DNA damage.
{ECO:0000256|HAMAP-Rule:MF_03140}.
-!- PTM: Phosphorylated. Phosphorylation upon DNA damage induces
relocalization to the nuclear plasma. {ECO:0000256|HAMAP-
Rule:MF_03140}.
-!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. FEN1
subfamily. {ECO:0000256|HAMAP-Rule:MF_03140}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation
of feature annotation. {ECO:0000256|HAMAP-Rule:MF_03140}.
-!- CAUTION: The sequence shown here is derived from an
EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
preliminary data. {ECO:0000313|EMBL:CCD16055.1}.
-----------------------------------------------------------------------
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EMBL; CAEQ01002148; CCD16055.1; -; Genomic_DNA.
Proteomes; UP000000702; Unassembled WGS sequence.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
GO; GO:0008409; F:5'-3' exonuclease activity; IEA:UniProtKB-UniRule.
GO; GO:0017108; F:5'-flap endonuclease activity; IEA:UniProtKB-UniRule.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
GO; GO:0006284; P:base-excision repair; IEA:UniProtKB-UniRule.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
GO; GO:0043137; P:DNA replication, removal of RNA primer; IEA:UniProtKB-UniRule.
CDD; cd09867; PIN_FEN1; 1.
HAMAP; MF_00614; Fen; 1.
InterPro; IPR036279; 5-3_exonuclease_C_sf.
InterPro; IPR023426; Flap_endonuc.
InterPro; IPR008918; HhH2.
InterPro; IPR029060; PIN-like_dom_sf.
InterPro; IPR006086; XPG-I_dom.
InterPro; IPR006084; XPG/Rad2.
InterPro; IPR019974; XPG_CS.
InterPro; IPR006085; XPG_DNA_repair_N.
PANTHER; PTHR11081; PTHR11081; 1.
Pfam; PF00867; XPG_I; 1.
Pfam; PF00752; XPG_N; 1.
PRINTS; PR00853; XPGRADSUPER.
SMART; SM00279; HhH2; 1.
SMART; SM00484; XPGI; 1.
SMART; SM00485; XPGN; 1.
SUPFAM; SSF47807; SSF47807; 1.
SUPFAM; SSF88723; SSF88723; 1.
PROSITE; PS00841; XPG_1; 1.
PROSITE; PS00842; XPG_2; 1.
3: Inferred from homology;
Coiled coil {ECO:0000256|SAM:Coils};
Complete proteome {ECO:0000313|Proteomes:UP000000702};
DNA damage {ECO:0000256|HAMAP-Rule:MF_03140};
DNA repair {ECO:0000256|HAMAP-Rule:MF_03140};
DNA replication {ECO:0000256|HAMAP-Rule:MF_03140};
Endonuclease {ECO:0000256|HAMAP-Rule:MF_03140};
Exonuclease {ECO:0000256|HAMAP-Rule:MF_03140};
Hydrolase {ECO:0000256|HAMAP-Rule:MF_03140};
Magnesium {ECO:0000256|HAMAP-Rule:MF_03140};
Membrane {ECO:0000256|SAM:Phobius};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_03140};
Mitochondrion {ECO:0000256|HAMAP-Rule:MF_03140,
ECO:0000256|SAAS:SAAS00882738};
Nuclease {ECO:0000256|HAMAP-Rule:MF_03140};
Nucleus {ECO:0000256|HAMAP-Rule:MF_03140,
ECO:0000256|SAAS:SAAS00022948};
Phosphoprotein {ECO:0000256|HAMAP-Rule:MF_03140};
Reference proteome {ECO:0000313|Proteomes:UP000000702};
Transmembrane {ECO:0000256|SAM:Phobius};
Transmembrane helix {ECO:0000256|SAM:Phobius}.
TRANSMEM 7 25 Helical. {ECO:0000256|SAM:Phobius}.
TRANSMEM 448 470 Helical. {ECO:0000256|SAM:Phobius}.
DOMAIN 41 151 XPGN. {ECO:0000259|SMART:SM00485}.
DOMAIN 190 262 XPGI. {ECO:0000259|SMART:SM00484}.
REGION 166 297 I-domain. {ECO:0000256|HAMAP-
Rule:MF_03140}.
REGION 380 388 Interaction with PCNA.
{ECO:0000256|HAMAP-Rule:MF_03140}.
COILED 138 168 {ECO:0000256|SAM:Coils}.
METAL 74 74 Magnesium 1. {ECO:0000256|HAMAP-
Rule:MF_03140}.
METAL 130 130 Magnesium 1. {ECO:0000256|HAMAP-
Rule:MF_03140}.
METAL 202 202 Magnesium 1. {ECO:0000256|HAMAP-
Rule:MF_03140}.
METAL 204 204 Magnesium 1. {ECO:0000256|HAMAP-
Rule:MF_03140}.
METAL 223 223 Magnesium 2. {ECO:0000256|HAMAP-
Rule:MF_03140}.
METAL 225 225 Magnesium 2. {ECO:0000256|HAMAP-
Rule:MF_03140}.
METAL 277 277 Magnesium 2. {ECO:0000256|HAMAP-
Rule:MF_03140}.
BINDING 114 114 DNA substrate. {ECO:0000256|HAMAP-
Rule:MF_03140}.
BINDING 202 202 DNA substrate. {ECO:0000256|HAMAP-
Rule:MF_03140}.
BINDING 275 275 DNA substrate. {ECO:0000256|HAMAP-
Rule:MF_03140}.
BINDING 277 277 DNA substrate. {ECO:0000256|HAMAP-
Rule:MF_03140}.
SEQUENCE 492 AA; 55669 MW; 731ED1C17126C002 CRC64;
MPTLNSLLRR ADLPFVSCVI SLLILSRLMP LQFTALLLGT MGVLGLSKLL YDRAPGAIKE
KELKCYFGRR IAIDASMAVY QFVIAMKGFQ EGQSVELTND AGEVTSHLNG IFFRTLRMID
EGLRPIYVFD GKPPSLKNSE LDSRRQRAEE AKHEYEKAKE EGDDEAMEKM SKRMVRVSRE
QMDEVKTLLQ LMGIPVVQAP SEAEAQCAEL VRKDKAWAVG TEDMDALAFG ARVMLRHLTY
GEAKKRPIAE YHLEDILELA GMTMEQFIDL CILLGCDYVP KIPGIGPHKA WEGIKKYGSM
EAFLESLDGT KYVVPEGFNY VEARNFFLHP EVTPGEEIEI QFREPDEEGL VKFLVQEKLF
NKDRVLKGIQ RLRDALAKKT QGRLDQFFTI TKVARPAAAE LTAAAGSKRS RSAVSCLGCS
NVKHLPVTRK RSKSNTRRSI DHVLYTNYPF TIFLFIYTYT YTYTYIYIYL KLAIDPCPLH
SSIQPCFSDT GS


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