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Flap endonuclease GEN (EC 3.1.-.-) (Flap structure-specific endonuclease GEN) (Xpg-like endonuclease) (DmGEN)

 GEN_DROME               Reviewed;         726 AA.
Q9VRJ0; Q9U9Q6;
15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
12-SEP-2018, entry version 119.
RecName: Full=Flap endonuclease GEN;
EC=3.1.-.-;
AltName: Full=Flap structure-specific endonuclease GEN;
AltName: Full=Xpg-like endonuclease;
Short=DmGEN;
Name=Gen; ORFNames=CG10670;
Drosophila melanogaster (Fruit fly).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophila; Sophophora.
NCBI_TaxID=7227;
[1]
NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
PubMed=15576351; DOI=10.1093/nar/gkh962;
Ishikawa G., Kanai Y., Takata K., Takeuchi R., Shimanouchi K.,
Ruike T., Furukawa T., Kimura S., Sakaguchi K.;
"DmGEN, a novel RAD2 family endo-exonuclease from Drosophila
melanogaster.";
Nucleic Acids Res. 32:6251-6259(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
PubMed=10731132; DOI=10.1126/science.287.5461.2185;
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I.,
Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P.,
de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M.,
Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P.,
Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W.,
Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K.,
Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J.,
Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C.,
Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A.,
Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z.,
Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X.,
Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D.,
Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A.,
Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L.,
Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M.,
Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G.,
Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H.,
Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
Spier E., Spradling A.C., Stapleton M., Strong R., Sun E.,
Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X.,
Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J.,
Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A.,
Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L.,
Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X.,
Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[3]
GENOME REANNOTATION.
STRAIN=Berkeley;
PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q.,
Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
Lewis S.E.;
"Annotation of the Drosophila melanogaster euchromatic genome: a
systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=Berkeley; TISSUE=Embryo, and Ovary;
PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M.,
George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H.,
Rubin G.M., Celniker S.E.;
"A Drosophila full-length cDNA resource.";
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
[5]
FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MUTAGENESIS OF
143-E--E-145, DEVELOPMENTAL STAGE, AND SUBCELLULAR LOCATION.
PubMed=17614965; DOI=10.1111/j.1742-4658.2007.05924.x;
Kanai Y., Ishikawa G., Takeuchi R., Ruike T., Nakamura R., Ihara A.,
Ohashi T., Takata K., Kimura S., Sakaguchi K.;
"DmGEN shows a flap endonuclease activity, cleaving the blocked-flap
structure and model replication fork.";
FEBS J. 274:3914-3927(2007).
[6]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-439, AND IDENTIFICATION
BY MASS SPECTROMETRY.
TISSUE=Embryo;
PubMed=18327897; DOI=10.1021/pr700696a;
Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P.;
"Phosphoproteome analysis of Drosophila melanogaster embryos.";
J. Proteome Res. 7:1675-1682(2008).
-!- FUNCTION: Endonuclease which cleaves flap structures at the
junction between single-stranded DNA and double-stranded DNA.
Specific for 5'-overhanging flap structures in which the 5'-
upstream of the flap is completely double-stranded. Prefers the
blocked-flap structures similar to those occurring at replication
forks, in which the 5' single-strand overhang of the flap is
double-stranded. Also possesses weak 5'- to 3'-exonuclease
activity on nicked but not gapped double-stranded DNA. Does not
cleave bubble-like or Holliday junction substrates.
{ECO:0000269|PubMed:15576351, ECO:0000269|PubMed:17614965}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Binds 2 magnesium ions per subunit. They probably participate
in the reaction catalyzed by the enzyme. May bind an additional
third magnesium ion after substrate binding. {ECO:0000250};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
pH dependence:
Optimum pH is 8. {ECO:0000269|PubMed:17614965};
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17614965}.
-!- DEVELOPMENTAL STAGE: Present in stage 1-4 embryos (at protein
level). {ECO:0000269|PubMed:17614965}.
-!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. GEN
subfamily. {ECO:0000305}.
-!- CAUTION: 3' to 5' exonuclease activity reported in PubMed:15576351
is probably artifactual, due to the presence of other nucleases in
the preparation. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AB103508; BAC57447.1; -; mRNA.
EMBL; AE014296; AAF50805.1; -; Genomic_DNA.
EMBL; AF160893; AAD46833.1; -; mRNA.
EMBL; AY128475; AAM75068.1; -; mRNA.
RefSeq; NP_647943.2; NM_139686.3.
UniGene; Dm.847; -.
ProteinModelPortal; Q9VRJ0; -.
SMR; Q9VRJ0; -.
IntAct; Q9VRJ0; 4.
STRING; 7227.FBpp0076879; -.
iPTMnet; Q9VRJ0; -.
PaxDb; Q9VRJ0; -.
PRIDE; Q9VRJ0; -.
EnsemblMetazoa; FBtr0077176; FBpp0076879; FBgn0263831.
GeneID; 38594; -.
KEGG; dme:Dmel_CG10670; -.
CTD; 38594; -.
FlyBase; FBgn0263831; Gen.
eggNOG; KOG2519; Eukaryota.
eggNOG; COG0258; LUCA.
GeneTree; ENSGT00640000091478; -.
InParanoid; Q9VRJ0; -.
KO; K15338; -.
OMA; GVKDLWN; -.
OrthoDB; EOG091G07ZH; -.
PhylomeDB; Q9VRJ0; -.
GenomeRNAi; 38594; -.
PRO; PR:Q9VRJ0; -.
Proteomes; UP000000803; Chromosome 3L.
Bgee; FBgn0263831; Expressed in 41 organ(s), highest expression level in embryo.
Genevisible; Q9VRJ0; DM.
GO; GO:0005737; C:cytoplasm; IDA:FlyBase.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0035312; F:5'-3' exodeoxyribonuclease activity; IDA:FlyBase.
GO; GO:0017108; F:5'-flap endonuclease activity; IDA:FlyBase.
GO; GO:0008821; F:crossover junction endodeoxyribonuclease activity; IDA:FlyBase.
GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:FlyBase.
GO; GO:0004520; F:endodeoxyribonuclease activity; IDA:FlyBase.
GO; GO:0004519; F:endonuclease activity; ISS:FlyBase.
GO; GO:0000400; F:four-way junction DNA binding; IDA:FlyBase.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008310; F:single-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:FlyBase.
GO; GO:0000737; P:DNA catabolic process, endonucleolytic; IDA:FlyBase.
GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IDA:FlyBase.
GO; GO:0006281; P:DNA repair; IMP:FlyBase.
GO; GO:0006302; P:double-strand break repair; IMP:FlyBase.
InterPro; IPR036279; 5-3_exonuclease_C_sf.
InterPro; IPR008918; HhH2.
InterPro; IPR029060; PIN-like_dom_sf.
InterPro; IPR006086; XPG-I_dom.
InterPro; IPR006084; XPG/Rad2.
InterPro; IPR006085; XPG_DNA_repair_N.
PANTHER; PTHR11081; PTHR11081; 1.
Pfam; PF00867; XPG_I; 1.
Pfam; PF00752; XPG_N; 1.
PRINTS; PR00853; XPGRADSUPER.
SMART; SM00279; HhH2; 1.
SMART; SM00484; XPGI; 1.
SMART; SM00485; XPGN; 1.
SUPFAM; SSF47807; SSF47807; 2.
SUPFAM; SSF88723; SSF88723; 1.
1: Evidence at protein level;
Complete proteome; DNA damage; DNA repair; Endonuclease; Exonuclease;
Hydrolase; Magnesium; Metal-binding; Nuclease; Nucleus;
Phosphoprotein; Reference proteome.
CHAIN 1 726 Flap endonuclease GEN.
/FTId=PRO_0000314148.
REGION 1 90 N-domain.
REGION 131 227 I-domain.
METAL 30 30 Magnesium 1. {ECO:0000250}.
METAL 74 74 Magnesium 1. {ECO:0000250}.
METAL 143 143 Magnesium 1. {ECO:0000250}.
METAL 145 145 Magnesium 1. {ECO:0000305}.
METAL 164 164 Magnesium 2. {ECO:0000250}.
METAL 166 166 Magnesium 2. {ECO:0000250}.
METAL 223 223 Magnesium 2. {ECO:0000250}.
MOD_RES 439 439 Phosphotyrosine.
{ECO:0000269|PubMed:18327897}.
MUTAGEN 143 145 EAE->AAA: Abolishes flap endonuclease
activity. {ECO:0000269|PubMed:17614965}.
CONFLICT 402 402 H -> L (in Ref. 1; BAC57447 and 4;
AAD46833). {ECO:0000305}.
CONFLICT 614 614 N -> D (in Ref. 1; BAC57447 and 4;
AAD46833). {ECO:0000305}.
CONFLICT 680 680 D -> A (in Ref. 1; BAC57447 and 4;
AAD46833). {ECO:0000305}.
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


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