FEN11_ORYSJ
ID FEN11_ORYSJ Reviewed; 380 AA.
AC Q9SXQ6; A0A0P0WQE5; Q0DGD0; Q53WJ9;
DT 12-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 128.
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};
DE AltName: Full=OsFEN-1 {ECO:0000303|PubMed:11851910};
DE AltName: Full=OsFEN-1a;
GN Name=FEN1A {ECO:0000305}; OrderedLocusNames=Os05g0540100, LOC_Os05g46270;
GN ORFNames=OsJ_19381, OSJNBa0052K01.23;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, COFACTOR, AND
RP ACTIVITY REGULATION.
RC STRAIN=cv. Nipponbare; TISSUE=Meristem;
RX PubMed=10798612; DOI=10.1023/a:1006349511964;
RA Kimura S., Ueda T., Hatanaka M., Takenouchi M., Hashimoto J., Sakaguchi K.;
RT "Plant homologue of flap endonuclease-1: molecular cloning,
RT characterization, and evidence of expression in meristematic tissues.";
RL Plant Mol. Biol. 42:415-427(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP INTERACTION WITH PCNA, AND SUBCELLULAR LOCATION.
RX PubMed=11851910; DOI=10.1046/j.1365-313x.2001.01184.x;
RA Kimura S., Suzuki T., Yanagawa Y., Yamamoto T., Nakagawa H., Tanaka I.,
RA Hashimoto J., Sakaguchi K.;
RT "Characterization of plant proliferating cell nuclear antigen (PCNA) and
RT flap endonuclease-1 (FEN-1), and their distribution in mitotic and meiotic
RT cell cycles.";
RL Plant J. 28:643-653(2001).
RN [8]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=14527718; DOI=10.1016/s0378-1119(03)00694-2;
RA Kimura S., Furukawa T., Kasai N., Mori Y., Kitamoto H.K., Sugawara F.,
RA Hashimoto J., Sakaguchi K.;
RT "Functional characterization of two flap endonuclease-1 homologues in
RT rice.";
RL Gene 314:63-71(2003).
RN [9]
RP INDUCTION BY GAMMA IRRADIATION.
RX PubMed=25124817; DOI=10.1093/jhered/esu025;
RA Hayashi G., Shibato J., Imanaka T., Cho K., Kubo A., Kikuchi S., Satoh K.,
RA Kimura S., Ozawa S., Fukutani S., Endo S., Ichikawa K., Agrawal G.K.,
RA Shioda S., Fukumoto M., Rakwal R.;
RT "Unraveling low-level gamma radiation--responsive changes in expression of
RT early and late genes in leaves of rice seedlings at Iitate Village,
RT Fukushima.";
RL J. Hered. 105:723-738(2014).
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 (By similarity). May be required for cell
CC proliferation. {ECO:0000255|HAMAP-Rule:MF_03140,
CC ECO:0000269|PubMed:10798612, ECO:0000269|PubMed:14527718}.
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 -!- ACTIVITY REGULATION: Inhibited by NaCl. {ECO:0000269|PubMed:10798612}.
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, ECO:0000269|PubMed:11851910}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000255|HAMAP-
CC Rule:MF_03140, ECO:0000269|PubMed:11851910}. Nucleus, nucleoplasm
CC {ECO:0000255|HAMAP-Rule:MF_03140}. Mitochondrion {ECO:0000255|HAMAP-
CC Rule:MF_03140}. Note=Resides mostly in the nucleoli and relocalizes to
CC the nucleoplasm upon DNA damage. {ECO:0000255|HAMAP-Rule:MF_03140}.
CC -!- TISSUE SPECIFICITY: Strongly expressed in proliferating tissues: root
CC and shoot apical meristem, tiller bud, leaf, ligule primordia, marginal
CC meristem of young leaves and panicles. Not expressed in mature leaves
CC when exposed to UV. {ECO:0000269|PubMed:10798612,
CC ECO:0000269|PubMed:14527718}.
CC -!- INDUCTION: Induced by gamma irradiation. {ECO:0000269|PubMed:25124817}.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAV59413.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB021666; BAA36171.1; -; mRNA.
DR EMBL; AC119291; AAV59413.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008211; BAF18093.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS95109.1; -; Genomic_DNA.
DR EMBL; CM000142; EEE64530.1; -; Genomic_DNA.
DR RefSeq; XP_015639321.1; XM_015783835.1.
DR AlphaFoldDB; Q9SXQ6; -.
DR SMR; Q9SXQ6; -.
DR STRING; 4530.OS05T0540100-01; -.
DR PaxDb; Q9SXQ6; -.
DR PRIDE; Q9SXQ6; -.
DR EnsemblPlants; Os05t0540100-01; Os05t0540100-01; Os05g0540100.
DR GeneID; 4339464; -.
DR Gramene; Os05t0540100-01; Os05t0540100-01; Os05g0540100.
DR KEGG; osa:4339464; -.
DR eggNOG; KOG2519; Eukaryota.
DR HOGENOM; CLU_032444_2_0_1; -.
DR InParanoid; Q9SXQ6; -.
DR OMA; GSQDYDS; -.
DR OrthoDB; 1094524at2759; -.
DR PlantReactome; R-OSA-9675782; Maturation.
DR Proteomes; UP000000763; Chromosome 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR ExpressionAtlas; Q9SXQ6; baseline and differential.
DR Genevisible; Q9SXQ6; OS.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
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 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 1: Evidence at protein level;
KW DNA damage; DNA repair; DNA replication; Endonuclease; Exonuclease;
KW Hydrolase; Magnesium; Metal-binding; Mitochondrion; Nuclease; Nucleus;
KW Phosphoprotein; Reference proteome.
FT CHAIN 1..380
FT /note="Flap endonuclease 1-A"
FT /id="PRO_0000154071"
FT REGION 1..105
FT /note="N-domain"
FT REGION 123..254
FT /note="I-domain"
FT REGION 336..344
FT /note="Interaction with PCNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03140"
FT REGION 351..380
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 380 AA; 42792 MW; E0148AAFA95A7364 CRC64;
MGIKGLTKLL ADNAPKAMKE QKFESYFGRR IAVDASMSIY QFLIVVGRTG METLTNEAGE
VTSHLQGMFN RTIRLLEAGI KPVYVFDGKP PDLKKQELAK RYSKREDATK ELTEAVEEGD
KDAIEKFSKR TVKVTKQHNE ECKRLLRLMG VPVVEAPCEA EAECAALCIN DMVYAVASED
MDSLTFGAPR FLRHLMDPSS KKIPVMEFEV AKVLEELELT MDQFIDLCIL SGCDYCDSIK
GIGGQTALKL IRQHGSIESI LENINKDRYQ IPEDWPYQEA RRLFKEPNVT LDIPELKWNA
PDEEGLVEFL VKENGFNQDR VTKAIEKIKF AKNKSSQGRL ESFFKPVVST SVPLKRKDTS
EKPTKAVANK KTKGAGGKKK
