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FEN11_PHYPA
ID   FEN11_PHYPA             Reviewed;         394 AA.
AC   A9S0B8;
DT   11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT   05-FEB-2008, sequence version 1.
DT   03-AUG-2022, entry version 87.
DE   RecName: Full=Flap endonuclease 1-A {ECO:0000255|HAMAP-Rule:MF_03140};
DE            Short=FEN-1-A {ECO:0000255|HAMAP-Rule:MF_03140};
DE            EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_03140};
DE   AltName: Full=Flap structure-specific endonuclease 1-A {ECO:0000255|HAMAP-Rule:MF_03140};
GN   Name=FEN1-A {ECO:0000255|HAMAP-Rule:MF_03140}; ORFNames=PHYPADRAFT_207454;
OS   Physcomitrium patens (Spreading-leaved earth moss) (Physcomitrella patens).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta;
OC   Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrium.
OX   NCBI_TaxID=3218;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Gransden 2004;
RX   PubMed=18079367; DOI=10.1126/science.1150646;
RA   Rensing S.A., Lang D., Zimmer A.D., Terry A., Salamov A., Shapiro H.,
RA   Nishiyama T., Perroud P.-F., Lindquist E.A., Kamisugi Y., Tanahashi T.,
RA   Sakakibara K., Fujita T., Oishi K., Shin-I T., Kuroki Y., Toyoda A.,
RA   Suzuki Y., Hashimoto S.-I., Yamaguchi K., Sugano S., Kohara Y.,
RA   Fujiyama A., Anterola A., Aoki S., Ashton N., Barbazuk W.B., Barker E.,
RA   Bennetzen J.L., Blankenship R., Cho S.H., Dutcher S.K., Estelle M.,
RA   Fawcett J.A., Gundlach H., Hanada K., Heyl A., Hicks K.A., Hughes J.,
RA   Lohr M., Mayer K., Melkozernov A., Murata T., Nelson D.R., Pils B.,
RA   Prigge M., Reiss B., Renner T., Rombauts S., Rushton P.J., Sanderfoot A.,
RA   Schween G., Shiu S.-H., Stueber K., Theodoulou F.L., Tu H., Van de Peer Y.,
RA   Verrier P.J., Waters E., Wood A., Yang L., Cove D., Cuming A.C., Hasebe M.,
RA   Lucas S., Mishler B.D., Reski R., Grigoriev I.V., Quatrano R.S.,
RA   Boore J.L.;
RT   "The Physcomitrella genome reveals evolutionary insights into the conquest
RT   of land by plants.";
RL   Science 319:64-69(2008).
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; DS544928; EDQ75281.1; -; Genomic_DNA.
DR   RefSeq; XP_001759777.1; XM_001759725.1.
DR   AlphaFoldDB; A9S0B8; -.
DR   SMR; A9S0B8; -.
DR   STRING; 3218.PP1S39_160V6.1; -.
DR   EnsemblPlants; Pp3c11_1310V3.1; Pp3c11_1310V3.1; Pp3c11_1310.
DR   EnsemblPlants; Pp3c11_1310V3.3; Pp3c11_1310V3.3; Pp3c11_1310.
DR   EnsemblPlants; Pp3c11_1310V3.4; Pp3c11_1310V3.4; Pp3c11_1310.
DR   Gramene; Pp3c11_1310V3.1; Pp3c11_1310V3.1; Pp3c11_1310.
DR   Gramene; Pp3c11_1310V3.3; Pp3c11_1310V3.3; Pp3c11_1310.
DR   Gramene; Pp3c11_1310V3.4; Pp3c11_1310V3.4; Pp3c11_1310.
DR   eggNOG; KOG2519; Eukaryota.
DR   HOGENOM; CLU_032444_2_0_1; -.
DR   InParanoid; A9S0B8; -.
DR   OMA; YVEAPCA; -.
DR   OrthoDB; 1094524at2759; -.
DR   Proteomes; UP000006727; Chromosome 11.
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:0008409; F:5'-3' exonuclease activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0017108; F:5'-flap endonuclease activity; IEA:UniProtKB-UniRule.
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   HAMAP; MF_00614; Fen; 1.
DR   InterPro; IPR002421; 5-3_exonuclease.
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; SM00475; 53EXOc; 1.
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..394
FT                   /note="Flap endonuclease 1-A"
FT                   /id="PRO_0000403526"
FT   REGION          1..105
FT                   /note="N-domain"
FT   REGION          123..254
FT                   /note="I-domain"
FT   REGION          338..346
FT                   /note="Interaction with PCNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT   REGION          343..394
FT                   /note="Disordered"
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         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   394 AA;  43651 MW;  D250A23CBF9D55C4 CRC64;
     MGIKGLTKLI ADNAHGAVKE QKFENYFGRK IAIDASMSIY QFLIVVGRSG SELLTNDAGE
     VTSHLQGMFN RTIRVLEAGL KPVYVFDGQP PDLKKRELAK RFARREDAAE DLVTAKETGN
     EADVEKYSKK TVKVTKQHNE DCRKLLRLMG VPVVEAPSEA EAECASLCKA EKVFAVASED
     MDSLTYGSTR FLRHLMEPTS RKLPVLEFDI AKVLEGLGLN MDQFVDLCIL CGCDYCDTIR
     GIGPQTALKM IRQHGSLEIV LENLNKDRYQ VPDPWPYQEA RRLFKEPLVT PPEKVPEFKW
     TAPDTEGLRQ LLVEENGFNN DRVMKAIEKL KVAKNKASQG RLESFFGVSS SSSNKRKEAP
     DSEASAGKQV KTAAAVKPAK AASKKGPAKG GKKK
 
 
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