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FEN1_USTMA
ID   FEN1_USTMA              Reviewed;         374 AA.
AC   Q4P1V1; A0A0D1CGS8;
DT   11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT   19-JUL-2005, sequence version 1.
DT   03-AUG-2022, entry version 100.
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}; ORFNames=UMAG_05912;
OS   Ustilago maydis (strain 521 / FGSC 9021) (Corn smut fungus).
OC   Eukaryota; Fungi; Dikarya; Basidiomycota; Ustilaginomycotina;
OC   Ustilaginomycetes; Ustilaginales; Ustilaginaceae; Ustilago.
OX   NCBI_TaxID=237631;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=521 / FGSC 9021;
RX   PubMed=17080091; DOI=10.1038/nature05248;
RA   Kaemper J., Kahmann R., Boelker M., Ma L.-J., Brefort T., Saville B.J.,
RA   Banuett F., Kronstad J.W., Gold S.E., Mueller O., Perlin M.H.,
RA   Woesten H.A.B., de Vries R., Ruiz-Herrera J., Reynaga-Pena C.G.,
RA   Snetselaar K., McCann M., Perez-Martin J., Feldbruegge M., Basse C.W.,
RA   Steinberg G., Ibeas J.I., Holloman W., Guzman P., Farman M.L.,
RA   Stajich J.E., Sentandreu R., Gonzalez-Prieto J.M., Kennell J.C., Molina L.,
RA   Schirawski J., Mendoza-Mendoza A., Greilinger D., Muench K., Roessel N.,
RA   Scherer M., Vranes M., Ladendorf O., Vincon V., Fuchs U., Sandrock B.,
RA   Meng S., Ho E.C.H., Cahill M.J., Boyce K.J., Klose J., Klosterman S.J.,
RA   Deelstra H.J., Ortiz-Castellanos L., Li W., Sanchez-Alonso P.,
RA   Schreier P.H., Haeuser-Hahn I., Vaupel M., Koopmann E., Friedrich G.,
RA   Voss H., Schlueter T., Margolis J., Platt D., Swimmer C., Gnirke A.,
RA   Chen F., Vysotskaia V., Mannhaupt G., Gueldener U., Muensterkoetter M.,
RA   Haase D., Oesterheld M., Mewes H.-W., Mauceli E.W., DeCaprio D., Wade C.M.,
RA   Butler J., Young S.K., Jaffe D.B., Calvo S.E., Nusbaum C., Galagan J.E.,
RA   Birren B.W.;
RT   "Insights from the genome of the biotrophic fungal plant pathogen Ustilago
RT   maydis.";
RL   Nature 444:97-101(2006).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=521 / FGSC 9021;
RA   Gueldener U., Muensterkoetter M., Walter M.C., Mannhaupt G., Kahmann R.;
RL   Submitted (SEP-2014) to the EMBL/GenBank/DDBJ databases.
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: Interacts with PCNA. Three molecules of FEN1 bind to one PCNA
CC       trimer with each molecule binding to one PCNA monomer. PCNA stimulates
CC       the nuclease activity without altering cleavage specificity.
CC       {ECO:0000255|HAMAP-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: Phosphorylated. Phosphorylation upon DNA damage induces
CC       relocalization to the nuclear plasma. {ECO:0000255|HAMAP-
CC       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; CM003159; KIS66173.1; -; Genomic_DNA.
DR   RefSeq; XP_011392252.1; XM_011393950.1.
DR   AlphaFoldDB; Q4P1V1; -.
DR   SMR; Q4P1V1; -.
DR   STRING; 5270.UM05912P0; -.
DR   EnsemblFungi; KIS66173; KIS66173; UMAG_05912.
DR   GeneID; 23565666; -.
DR   KEGG; uma:UMAG_05912; -.
DR   VEuPathDB; FungiDB:UMAG_05912; -.
DR   eggNOG; KOG2519; Eukaryota.
DR   HOGENOM; CLU_032444_2_0_1; -.
DR   InParanoid; Q4P1V1; -.
DR   OMA; GSQDYDS; -.
DR   OrthoDB; 1094524at2759; -.
DR   Proteomes; UP000000561; Chromosome 20.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0005829; C:cytosol; IEA:EnsemblFungi.
DR   GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR   GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR   GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0008409; F:5'-3' exonuclease activity; IBA:GO_Central.
DR   GO; GO:0017108; F:5'-flap endonuclease activity; IBA:GO_Central.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0006284; P:base-excision repair; IEA:UniProtKB-UniRule.
DR   GO; GO:0043137; P:DNA replication, removal of RNA primer; IEA:UniProtKB-UniRule.
DR   GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IEA:EnsemblFungi.
DR   GO; GO:0007534; P:gene conversion at mating-type locus; IEA:EnsemblFungi.
DR   GO; GO:0035753; P:maintenance of DNA trinucleotide repeats; IEA:EnsemblFungi.
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   3: Inferred from homology;
KW   DNA damage; DNA repair; DNA replication; Endonuclease; Exonuclease;
KW   Hydrolase; Magnesium; Metal-binding; Mitochondrion; Nuclease; Nucleus;
KW   Phosphoprotein; Reference proteome.
FT   CHAIN           1..374
FT                   /note="Flap endonuclease 1"
FT                   /id="PRO_0000403604"
FT   REGION          1..105
FT                   /note="N-domain"
FT   REGION          103..122
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          123..254
FT                   /note="I-domain"
FT   REGION          335..374
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          340..348
FT                   /note="Interaction with PCNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   COMPBIAS        356..374
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         71
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         87
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         159
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         159
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         161
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         180
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         182
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         232
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         234
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   BINDING         234
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
SQ   SEQUENCE   374 AA;  42304 MW;  5D362A9411D701AB CRC64;
     MGIKGLTALI SDEAPGAIKE MEIKTYFGRK VAIDASMSLY QFLIAVRQND GQQLMTESGE
     TTSHLLGFFY RTLRMIDYGI KPMYVFDGTP PDLKKELLQK RFGRREEARE QEEEQKDVAD
     AEKMDQLARR QVRPTRQHNE EVRHLLKLMG IPCVIAPSEA EAQCAELARA GKVYAAGSED
     MDTLTFGTPI LLKHLTASEQ KKLPVHQVDL AKALEGLQMT MAQFIDLCIL LGCDYLDPIK
     GIGPKTALKL IREHKTLENV VHHLKEDGKK SVQIPDHWPF QEARKIFESP DVQKGVDLDL
     KWEAPDVEAM VKFLCQDKGF SEDRVRKGCE KLQKSLSQKQ QGRLDGFFTV KPGSAPPKRK
     AEDDKKNVKK KGKK
 
 
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