FEN1_RAT
ID FEN1_RAT Reviewed; 380 AA.
AC Q5XIP6; Q9JHW7;
DT 11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Flap endonuclease 1 {ECO:0000255|HAMAP-Rule:MF_03140};
DE Short=FEN-1 {ECO:0000255|HAMAP-Rule:MF_03140};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_03140};
DE AltName: Full=Flap structure-specific endonuclease 1 {ECO:0000255|HAMAP-Rule:MF_03140};
GN Name=Fen1 {ECO:0000255|HAMAP-Rule:MF_03140};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Chen D., Cao G., Yang S., Li M., Chen J.;
RT "Cloning and characterization of a rat DNA structure-specific endonuclease
RT (Fen-1).";
RL Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
CC -!- FUNCTION: Structure-specific nuclease with 5'-flap endonuclease and 5'-
CC 3' exonuclease activities involved in DNA replication and repair.
CC During DNA replication, cleaves the 5'-overhanging flap structure that
CC is generated by displacement synthesis when DNA polymerase encounters
CC the 5'-end of a downstream Okazaki fragment. It enters the flap from
CC the 5'-end and then tracks to cleave the flap base, leaving a nick for
CC ligation. Also involved in the long patch base excision repair (LP-BER)
CC pathway, by cleaving within the apurinic/apyrimidinic (AP) site-
CC terminated flap. Acts as a genome stabilization factor that prevents
CC flaps from equilibrating into structures that lead to duplications and
CC deletions. Also possesses 5'-3' exonuclease activity on nicked or
CC gapped double-stranded DNA, and exhibits RNase H activity. Also
CC involved in replication and repair of rDNA and in repairing
CC mitochondrial DNA. {ECO:0000255|HAMAP-Rule:MF_03140}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03140};
CC Note=Binds 2 magnesium ions per subunit. They probably participate in
CC the reaction catalyzed by the enzyme. May bind an additional third
CC magnesium ion after substrate binding. {ECO:0000255|HAMAP-
CC Rule:MF_03140};
CC -!- SUBUNIT: Three molecules of FEN1 bind to one PCNA trimer with each
CC molecule binding to one PCNA monomer. PCNA stimulates the nuclease
CC activity without altering cleavage specificity. The C-terminal domain
CC binds EP300; can bind simultaneously to both PCNA and EP300. Interacts
CC with PCNA; can bind simultaneously to both PCNA and EP300. Interacts
CC with DDX11; this interaction is direct and increases flap endonuclease
CC activity of FEN1. Interacts with WDR4; regulating its endonuclease
CC activity. {ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
CC Rule:MF_03140}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000255|HAMAP-
CC Rule:MF_03140}. Nucleus, nucleoplasm {ECO:0000255|HAMAP-Rule:MF_03140}.
CC Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03140}. Note=Resides mostly in
CC the nucleoli and relocalizes to the nucleoplasm upon DNA damage.
CC {ECO:0000255|HAMAP-Rule:MF_03140}.
CC -!- PTM: Acetylated by EP300. Acetylation inhibits both endonuclease and
CC exonuclease activity. Acetylation also reduces DNA-binding activity but
CC does not affect interaction with PCNA or EP300. {ECO:0000255|HAMAP-
CC Rule:MF_03140}.
CC -!- PTM: Phosphorylation upon DNA damage induces relocalization to the
CC nuclear plasma. Phosphorylation at Ser-187 by CDK2 occurs during late
CC S-phase and results in dissociation from PCNA. {ECO:0000255|HAMAP-
CC Rule:MF_03140}.
CC -!- PTM: Methylation at Arg-192 by PRMT5 impedes Ser-187 phosphorylation
CC and increases interaction with PCNA. {ECO:0000255|HAMAP-Rule:MF_03140}.
CC -!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. FEN1
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_03140}.
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DR EMBL; AF281018; AAF81265.1; -; mRNA.
DR EMBL; CH473953; EDM12793.1; -; Genomic_DNA.
DR EMBL; BC083630; AAH83630.1; -; mRNA.
DR RefSeq; NP_445882.1; NM_053430.1.
DR RefSeq; XP_006231135.1; XM_006231073.3.
DR RefSeq; XP_006231136.1; XM_006231074.3.
DR RefSeq; XP_008758467.1; XM_008760245.2.
DR RefSeq; XP_008758468.1; XM_008760246.2.
DR AlphaFoldDB; Q5XIP6; -.
DR SMR; Q5XIP6; -.
DR IntAct; Q5XIP6; 1.
DR MINT; Q5XIP6; -.
DR STRING; 10116.ENSRNOP00000027842; -.
DR iPTMnet; Q5XIP6; -.
DR PhosphoSitePlus; Q5XIP6; -.
DR jPOST; Q5XIP6; -.
DR PaxDb; Q5XIP6; -.
DR PRIDE; Q5XIP6; -.
DR Ensembl; ENSRNOT00000027842; ENSRNOP00000027842; ENSRNOG00000020531.
DR Ensembl; ENSRNOT00000104683; ENSRNOP00000081266; ENSRNOG00000020531.
DR Ensembl; ENSRNOT00000106648; ENSRNOP00000078106; ENSRNOG00000020531.
DR GeneID; 84490; -.
DR KEGG; rno:84490; -.
DR CTD; 2237; -.
DR RGD; 621821; Fen1.
DR eggNOG; KOG2519; Eukaryota.
DR GeneTree; ENSGT00940000155807; -.
DR HOGENOM; CLU_032444_2_0_1; -.
DR InParanoid; Q5XIP6; -.
DR OMA; GSQDYDS; -.
DR OrthoDB; 1094524at2759; -.
DR PhylomeDB; Q5XIP6; -.
DR TreeFam; TF105701; -.
DR Reactome; R-RNO-110362; POLB-Dependent Long Patch Base Excision Repair.
DR Reactome; R-RNO-174437; Removal of the Flap Intermediate from the C-strand.
DR Reactome; R-RNO-5651801; PCNA-Dependent Long Patch Base Excision Repair.
DR Reactome; R-RNO-5685939; HDR through MMEJ (alt-NHEJ).
DR Reactome; R-RNO-69166; Removal of the Flap Intermediate.
DR PRO; PR:Q5XIP6; -.
DR Proteomes; UP000002494; Chromosome 1.
DR Proteomes; UP000234681; Chromosome 1.
DR Bgee; ENSRNOG00000020531; Expressed in thymus and 19 other tissues.
DR Genevisible; Q5XIP6; RN.
DR GO; GO:0000781; C:chromosome, telomeric region; IEA:Ensembl.
DR GO; GO:0005739; C:mitochondrion; ISO:RGD.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:RGD.
DR GO; GO:0032991; C:protein-containing complex; ISO:RGD.
DR GO; GO:0008409; F:5'-3' exonuclease activity; ISO:RGD.
DR GO; GO:0017108; F:5'-flap endonuclease activity; ISO:RGD.
DR GO; GO:0003677; F:DNA binding; ISO:RGD.
DR GO; GO:0004527; F:exonuclease activity; ISO:RGD.
DR GO; GO:0048256; F:flap endonuclease activity; ISO:RGD.
DR GO; GO:0000287; F:magnesium ion binding; ISO:RGD.
DR GO; GO:0030145; F:manganese ion binding; ISO:RGD.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; ISO:RGD.
DR GO; GO:0006284; P:base-excision repair; IEA:UniProtKB-UniRule.
DR GO; GO:0006281; P:DNA repair; ISO:RGD.
DR GO; GO:0006260; P:DNA replication; ISO:RGD.
DR GO; GO:0043137; P:DNA replication, removal of RNA primer; ISO:RGD.
DR GO; GO:0007613; P:memory; IMP:RGD.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; ISO:RGD.
DR GO; GO:0045876; P:positive regulation of sister chromatid cohesion; ISO:RGD.
DR HAMAP; MF_00614; Fen; 1.
DR InterPro; IPR036279; 5-3_exonuclease_C_sf.
DR InterPro; IPR023426; Flap_endonuc.
DR InterPro; IPR008918; HhH2.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR006086; XPG-I_dom.
DR InterPro; IPR006084; XPG/Rad2.
DR InterPro; IPR019974; XPG_CS.
DR InterPro; IPR006085; XPG_DNA_repair_N.
DR PANTHER; PTHR11081; PTHR11081; 1.
DR Pfam; PF00867; XPG_I; 1.
DR Pfam; PF00752; XPG_N; 1.
DR PRINTS; PR00853; XPGRADSUPER.
DR SMART; SM00279; HhH2; 1.
DR SMART; SM00484; XPGI; 1.
DR SMART; SM00485; XPGN; 1.
DR SUPFAM; SSF47807; SSF47807; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
DR PROSITE; PS00841; XPG_1; 1.
DR PROSITE; PS00842; XPG_2; 1.
PE 2: Evidence at transcript level;
KW Acetylation; DNA damage; DNA repair; DNA replication; Endonuclease;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Methylation;
KW Mitochondrion; Nuclease; Nucleus; Phosphoprotein; Reference proteome.
FT CHAIN 1..380
FT /note="Flap endonuclease 1"
FT /id="PRO_0000403485"
FT REGION 1..104
FT /note="N-domain"
FT REGION 122..253
FT /note="I-domain"
FT REGION 327..380
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 336..344
FT /note="Interaction with PCNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT COMPBIAS 328..342
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 352..366
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 34
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 47
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 70
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 86
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 158
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 158
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 160
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 179
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 231
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 233
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT BINDING 233
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT MOD_RES 19
FT /note="Symmetric dimethylarginine; by PRMT5"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 80
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 100
FT /note="Symmetric dimethylarginine; by PRMT5"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 104
FT /note="Symmetric dimethylarginine; by PRMT5"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 187
FT /note="Phosphoserine; by CDK2"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 192
FT /note="Symmetric dimethylarginine; by PRMT5"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 197
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P39748"
FT MOD_RES 255
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P39748"
FT MOD_RES 293
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P39748"
FT MOD_RES 335
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P39748"
FT MOD_RES 336
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P39748"
FT MOD_RES 354
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 375
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT MOD_RES 380
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P39748, ECO:0000255|HAMAP-
FT Rule:MF_03140"
FT CONFLICT 95..96
FT /note="GE -> AQ (in Ref. 1; AAF81265)"
FT /evidence="ECO:0000305"
FT CONFLICT 289
FT /note="L -> V (in Ref. 1; AAF81265)"
FT /evidence="ECO:0000305"
FT CONFLICT 372
FT /note="G -> A (in Ref. 1; AAF81265)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 380 AA; 42609 MW; 3732F5FF0E121670 CRC64;
MGIQGLAKLI ADVAPSAIRE NDIKSYFGRK VAIDASMSIY QFLIAVRQGG DVLQNEEGET
TSHLMGMFYR TIRMMENGIK PVYIFDGKPP QLKSGELAKR SERRAEAEKQ LQQAQEAGAE
EEVEKFTKRL VKVTKQHNDE CKHLLSLMGI PYLDAPSEAE ASCAALAKAG KVYAAATEDM
DCLTFGSPVL MRHLTASEAK KLPIQEFHLS RVLQELGLNQ EQFVDLCILL GSDYCESVRG
IGPKRAVDLI QKHKSIEEIV RRLDPSKYPV PENWLHKEAR QLFLEPEVLD PESVELKWSE
PNEEELVKFM CGEKQFSEER IRSGVKRLNK SRQGSTQGRL DDFFKVTGSL SSAKRKEPEP
KGPAKKKAKT GGAGKFRRGK
