GEN_DROME
ID GEN_DROME Reviewed; 726 AA.
AC Q9VRJ0; Q9U9Q6;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Flap endonuclease GEN;
DE EC=3.1.-.-;
DE AltName: Full=Flap structure-specific endonuclease GEN;
DE AltName: Full=Xpg-like endonuclease;
DE Short=DmGEN;
GN Name=Gen; ORFNames=CG10670;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RX PubMed=15576351; DOI=10.1093/nar/gkh962;
RA Ishikawa G., Kanai Y., Takata K., Takeuchi R., Shimanouchi K., Ruike T.,
RA Furukawa T., Kimura S., Sakaguchi K.;
RT "DmGEN, a novel RAD2 family endo-exonuclease from Drosophila
RT melanogaster.";
RL Nucleic Acids Res. 32:6251-6259(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley; TISSUE=Embryo, and Ovary;
RX PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
RA Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A.,
RA Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M.,
RA Celniker S.E.;
RT "A Drosophila full-length cDNA resource.";
RL Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
RN [5]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MUTAGENESIS OF
RP 143-E--E-145, DEVELOPMENTAL STAGE, AND SUBCELLULAR LOCATION.
RX PubMed=17614965; DOI=10.1111/j.1742-4658.2007.05924.x;
RA Kanai Y., Ishikawa G., Takeuchi R., Ruike T., Nakamura R., Ihara A.,
RA Ohashi T., Takata K., Kimura S., Sakaguchi K.;
RT "DmGEN shows a flap endonuclease activity, cleaving the blocked-flap
RT structure and model replication fork.";
RL FEBS J. 274:3914-3927(2007).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-439, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RC TISSUE=Embryo;
RX PubMed=18327897; DOI=10.1021/pr700696a;
RA Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P.;
RT "Phosphoproteome analysis of Drosophila melanogaster embryos.";
RL J. Proteome Res. 7:1675-1682(2008).
CC -!- FUNCTION: Endonuclease which cleaves flap structures at the junction
CC between single-stranded DNA and double-stranded DNA. Specific for 5'-
CC overhanging flap structures in which the 5'-upstream of the flap is
CC completely double-stranded. Prefers the blocked-flap structures similar
CC to those occurring at replication forks, in which the 5' single-strand
CC overhang of the flap is double-stranded. Also possesses weak 5'- to 3'-
CC exonuclease activity on nicked but not gapped double-stranded DNA. Does
CC not cleave bubble-like or Holliday junction substrates.
CC {ECO:0000269|PubMed:15576351, ECO:0000269|PubMed:17614965}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
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:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:17614965};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17614965}.
CC -!- DEVELOPMENTAL STAGE: Present in stage 1-4 embryos (at protein level).
CC {ECO:0000269|PubMed:17614965}.
CC -!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. GEN subfamily.
CC {ECO:0000305}.
CC -!- CAUTION: 3' to 5' exonuclease activity reported in PubMed:15576351 is
CC probably artifactual, due to the presence of other nucleases in the
CC preparation. {ECO:0000305}.
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DR EMBL; AB103508; BAC57447.1; -; mRNA.
DR EMBL; AE014296; AAF50805.1; -; Genomic_DNA.
DR EMBL; AF160893; AAD46833.1; -; mRNA.
DR EMBL; AY128475; AAM75068.1; -; mRNA.
DR RefSeq; NP_647943.2; NM_139686.3.
DR AlphaFoldDB; Q9VRJ0; -.
DR SMR; Q9VRJ0; -.
DR BioGRID; 64062; 2.
DR IntAct; Q9VRJ0; 4.
DR STRING; 7227.FBpp0076879; -.
DR iPTMnet; Q9VRJ0; -.
DR PaxDb; Q9VRJ0; -.
DR DNASU; 38594; -.
DR EnsemblMetazoa; FBtr0077176; FBpp0076879; FBgn0263831.
DR GeneID; 38594; -.
DR KEGG; dme:Dmel_CG10670; -.
DR CTD; 38594; -.
DR FlyBase; FBgn0263831; Gen.
DR VEuPathDB; VectorBase:FBgn0263831; -.
DR eggNOG; KOG2519; Eukaryota.
DR GeneTree; ENSGT00940000159266; -.
DR HOGENOM; CLU_013777_2_0_1; -.
DR InParanoid; Q9VRJ0; -.
DR OMA; MCAYLNE; -.
DR OrthoDB; 1094524at2759; -.
DR PhylomeDB; Q9VRJ0; -.
DR SignaLink; Q9VRJ0; -.
DR BioGRID-ORCS; 38594; 0 hits in 1 CRISPR screen.
DR GenomeRNAi; 38594; -.
DR PRO; PR:Q9VRJ0; -.
DR Proteomes; UP000000803; Chromosome 3L.
DR Bgee; FBgn0263831; Expressed in dorsal head epidermis anlage (Drosophila) and 23 other tissues.
DR Genevisible; Q9VRJ0; DM.
DR GO; GO:0005737; C:cytoplasm; IDA:FlyBase.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0035312; F:5'-3' exodeoxyribonuclease activity; IDA:FlyBase.
DR GO; GO:0017108; F:5'-flap endonuclease activity; IDA:FlyBase.
DR GO; GO:0008821; F:crossover junction endodeoxyribonuclease activity; IDA:FlyBase.
DR GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:FlyBase.
DR GO; GO:0004520; F:endodeoxyribonuclease activity; IDA:FlyBase.
DR GO; GO:0004519; F:endonuclease activity; ISS:FlyBase.
DR GO; GO:0000400; F:four-way junction DNA binding; IDA:FlyBase.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008310; F:single-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:FlyBase.
DR GO; GO:0000737; P:DNA catabolic process, endonucleolytic; IDA:FlyBase.
DR GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IDA:FlyBase.
DR GO; GO:0006281; P:DNA repair; IMP:FlyBase.
DR GO; GO:0006302; P:double-strand break repair; IMP:FlyBase.
DR InterPro; IPR036279; 5-3_exonuclease_C_sf.
DR InterPro; IPR041012; GEN_chromo.
DR InterPro; IPR008918; HhH2.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR006086; XPG-I_dom.
DR InterPro; IPR006084; XPG/Rad2.
DR InterPro; IPR006085; XPG_DNA_repair_N.
DR PANTHER; PTHR11081; PTHR11081; 1.
DR Pfam; PF18704; Chromo_2; 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.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; Endonuclease; Exonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Nucleus; Phosphoprotein; Reference proteome.
FT CHAIN 1..726
FT /note="Flap endonuclease GEN"
FT /id="PRO_0000314148"
FT REGION 1..90
FT /note="N-domain"
FT REGION 96..116
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 131..227
FT /note="I-domain"
FT REGION 478..521
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 704..726
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 99..113
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 485..512
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 709..726
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 30
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 74
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 143
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 145
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 164
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 166
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT MOD_RES 439
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000269|PubMed:18327897"
FT MUTAGEN 143..145
FT /note="EAE->AAA: Abolishes flap endonuclease activity."
FT /evidence="ECO:0000269|PubMed:17614965"
FT CONFLICT 402
FT /note="H -> L (in Ref. 1; BAC57447 and 4; AAD46833)"
FT /evidence="ECO:0000305"
FT CONFLICT 614
FT /note="N -> D (in Ref. 1; BAC57447 and 4; AAD46833)"
FT /evidence="ECO:0000305"
FT CONFLICT 680
FT /note="D -> A (in Ref. 1; BAC57447 and 4; AAD46833)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 726 AA; 82534 MW; 94107D2C7787F529 CRC64;
MGVKELWGVL TPHCERKPIN ELRGKKVAID LAGWVCESLN VVDYFVHPRH HLKNLFFRTC
YLIWEQVTPV FVLEGVAPKL KSQVIAKRNE LQFRGVKPKN SPECTQSQPS KGDKGRSRFN
HVLKQCETLL LSMGIQCVQG PGEAEAYCAF LNKHGLVDGV ISQDSDCFAY GAVRVYRNFS
VSTQGAQAAA GGAVDIYDMR EITSRMDFGQ QKIIVMALLC GCDYCPDGIG GIGKDGVLKL
FNKYKETEIL DRMRSWRGET DKYNALEIRV DDKSICSNCG HIGKTQSHTK SGCSVCRTHK
GCDESLWKEQ RLSIKSELTL RRKALLSPDF PNEEIIAEFL SEPDTIPNLN LNWRQPNLVK
FIKQIGHLLQ WPEIYCFQKF FPILTRWQVQ QSKQEKILIQ PHEIIKKRTV KGVPSLELRW
HDPSGIFKGL IPDKQIAEYE AEHPKGIEEL YYTIEPLDML ETAYPDLVAA FLKSKEKPAK
KTTRKKKTAS EEENKENEPN SKPKRVVRKI KAQPEENQPL LHQFLGRKKE GTPVKAPAPQ
RQQCSTPITK FLPSDLESDC DAEEFDMSDI VKGIISNPNA KPALTNHDGH QLHYEPMAED
LSLRLAQMSL GNVNESPKVE TKRDLSQVDQ LPQSKRFSLE DSFDLLVKGD LQKLARTPVE
RFKMQHRISE KIPTPVKPLD NISYFFNQSS DNADVFEELM NSSLVPQDQE DNAEDEEEDD
LVVISD
