XPF_DROME
ID XPF_DROME Reviewed; 961 AA.
AC Q24087; Q8IHB9; Q9W4L3;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 30-AUG-2005, sequence version 2.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=DNA repair endonuclease XPF;
DE EC=3.1.-.-;
DE AltName: Full=Protein meiotic 9;
GN Name=mei-9; ORFNames=CG3697;
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 [GENOMIC DNA].
RX PubMed=8647398; DOI=10.1093/genetics/141.2.619;
RA Sekelsky J.J., McKim K.S., Chin G.M., Hawley R.S.;
RT "The Drosophila meiotic recombination gene mei-9 encodes a homologue of the
RT yeast excision repair protein Rad1.";
RL Genetics 141:619-627(1995).
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=Testis;
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 INTERACTION WITH HDM.
RX PubMed=18957705; DOI=10.1534/genetics.108.093104;
RA Joyce E.F., Tanneti S.N., McKim K.S.;
RT "Drosophila hold'em is required for a subset of meiotic crossovers and
RT interacts with the dna repair endonuclease complex subunits MEI-9 and
RT ERCC1.";
RL Genetics 181:335-340(2009).
CC -!- FUNCTION: Implicated in recombination events during meiosis, mostly in
CC meiotic exchange. May directly resolve Holliday junctions within
CC recombination intermediates leading to DNA exchange. Also required for
CC the repair of mismatches within meiotic heteroduplex DNA and for
CC nucleotide excision repair.
CC -!- SUBUNIT: Heterodimer (By similarity). Interacts with hdm. {ECO:0000250,
CC ECO:0000269|PubMed:18957705}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the XPF family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC46917.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U27181; AAC46917.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AE014298; AAF45938.1; -; Genomic_DNA.
DR EMBL; BT001319; AAN71074.1; -; mRNA.
DR PIR; S58936; S58936.
DR RefSeq; NP_001284859.1; NM_001297930.1.
DR RefSeq; NP_525068.1; NM_080329.3.
DR AlphaFoldDB; Q24087; -.
DR SMR; Q24087; -.
DR BioGRID; 57890; 5.
DR IntAct; Q24087; 2.
DR STRING; 7227.FBpp0070624; -.
DR PaxDb; Q24087; -.
DR EnsemblMetazoa; FBtr0070656; FBpp0070624; FBgn0002707.
DR EnsemblMetazoa; FBtr0343574; FBpp0310174; FBgn0002707.
DR GeneID; 31373; -.
DR KEGG; dme:Dmel_CG3697; -.
DR CTD; 31373; -.
DR FlyBase; FBgn0002707; mei-9.
DR VEuPathDB; VectorBase:FBgn0002707; -.
DR eggNOG; KOG0442; Eukaryota.
DR HOGENOM; CLU_002265_1_0_1; -.
DR InParanoid; Q24087; -.
DR OMA; FHKILQA; -.
DR OrthoDB; 324863at2759; -.
DR PhylomeDB; Q24087; -.
DR Reactome; R-DME-5696395; Formation of Incision Complex in GG-NER.
DR Reactome; R-DME-5696400; Dual Incision in GG-NER.
DR Reactome; R-DME-6782135; Dual incision in TC-NER.
DR BioGRID-ORCS; 31373; 0 hits in 1 CRISPR screen.
DR GenomeRNAi; 31373; -.
DR PRO; PR:Q24087; -.
DR Proteomes; UP000000803; Chromosome X.
DR Bgee; FBgn0002707; Expressed in cleaving embryo and 16 other tissues.
DR ExpressionAtlas; Q24087; baseline and differential.
DR Genevisible; Q24087; DM.
DR GO; GO:0000110; C:nucleotide-excision repair factor 1 complex; IBA:GO_Central.
DR GO; GO:0032991; C:protein-containing complex; IDA:FlyBase.
DR GO; GO:0003684; F:damaged DNA binding; IBA:GO_Central.
DR GO; GO:0046982; F:protein heterodimerization activity; IPI:FlyBase.
DR GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0000014; F:single-stranded DNA endodeoxyribonuclease activity; IBA:GO_Central.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IMP:FlyBase.
DR GO; GO:0006310; P:DNA recombination; TAS:FlyBase.
DR GO; GO:0006302; P:double-strand break repair; IMP:FlyBase.
DR GO; GO:0000724; P:double-strand break repair via homologous recombination; IBA:GO_Central.
DR GO; GO:0016321; P:female meiosis chromosome segregation; IMP:FlyBase.
DR GO; GO:0007143; P:female meiotic nuclear division; IMP:FlyBase.
DR GO; GO:0045132; P:meiotic chromosome segregation; IMP:FlyBase.
DR GO; GO:0006298; P:mismatch repair; IMP:FlyBase.
DR GO; GO:0006289; P:nucleotide-excision repair; IMP:FlyBase.
DR GO; GO:1901255; P:nucleotide-excision repair involved in interstrand cross-link repair; IBA:GO_Central.
DR GO; GO:0006296; P:nucleotide-excision repair, DNA incision, 5'-to lesion; IBA:GO_Central.
DR GO; GO:0030716; P:oocyte fate determination; IMP:FlyBase.
DR GO; GO:0007131; P:reciprocal meiotic recombination; IMP:FlyBase.
DR GO; GO:0000712; P:resolution of meiotic recombination intermediates; IMP:FlyBase.
DR InterPro; IPR006166; ERCC4_domain.
DR InterPro; IPR011335; Restrct_endonuc-II-like.
DR InterPro; IPR010994; RuvA_2-like.
DR InterPro; IPR006167; XPF.
DR Pfam; PF02732; ERCC4; 1.
DR SMART; SM00891; ERCC4; 1.
DR SUPFAM; SSF47781; SSF47781; 1.
DR SUPFAM; SSF52980; SSF52980; 1.
DR TIGRFAMs; TIGR00596; rad1; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; DNA-binding; Endonuclease; Hydrolase; Meiosis;
KW Nuclease; Nucleus; Reference proteome.
FT CHAIN 1..961
FT /note="DNA repair endonuclease XPF"
FT /id="PRO_0000198855"
FT DOMAIN 697..777
FT /note="ERCC4"
FT REGION 1..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 451..485
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 674..693
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 451..467
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 115
FT /note="V -> G (in Ref. 1; AAC46917)"
FT /evidence="ECO:0000305"
FT CONFLICT 286
FT /note="S -> T (in Ref. 1; AAC46917 and 4; AAN71074)"
FT /evidence="ECO:0000305"
FT CONFLICT 318
FT /note="S -> T (in Ref. 1; AAC46917)"
FT /evidence="ECO:0000305"
FT CONFLICT 594
FT /note="A -> P (in Ref. 1; AAC46917)"
FT /evidence="ECO:0000305"
FT CONFLICT 798
FT /note="A -> R (in Ref. 1; AAC46917)"
FT /evidence="ECO:0000305"
FT CONFLICT 853
FT /note="T -> M (in Ref. 1; AAC46917 and 4; AAN71074)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 961 AA; 109519 MW; 00099A7E52B3FC46 CRC64;
MADSCAENAA KGTENERPKE VEASADTVPQ VEEGVEEYLK RKNMVLLDYE KQMFLDLVEA
DGLLVCAKGL SYDRVVISIL KAYSDSGNLV LVINSSDWEE QYYKSKIEPK YVHEVASTAT
ERERVYLEGG LQFISTRILV VDLLKQRIPI ELISGIIVLR AHTIIESCQE AFALRLFRQK
NKTGFVKAFS SSPEAFTIGY SHVERTMRNL FVKHLYIWPR FHESVRTVLQ PWKIQSIEMH
VPISQNITSI QSHILEIMNF LVQEIKRINR TVDMEAVTVE NCVTKSFHKI LQAQLDCIWH
QLNSQTKLIV ADLKILRSLM ISTMYHDAVS AYAFMKRYRS TEYALSNSGW TLLDAAEQIF
KLSRQRVFNG QQEFEPEPCP KWQTLTDLLT KEIPGDMRRS RRSEQQPKVL ILCQDARTCH
QLKQYLTQGG PRFLLQQALQ HEVPVGKLSD NYAKESQTRS APPKNVSSNK ELRREEVSGS
QPPLAGMDEL AQLLSESETE GQHFEESYML TMTQPVEVGP AAIDIKPDPD VSIFETIPEL
EQFDVTAALA SVPHQPYICL QTFKTEREGS MALEHMLEQL QPHYVVMYNM NVTAIRQLEV
FEARRRLPPA DRMKVYFLIH ARTVEEQAYL TSLRREKAAF EFIIDTKSKM VIPKYQDGKT
DEAFLLLKTY DDEPTDENAK SRQAGGQAPQ ATKETPKVIV DMREFRSDLP CLIHKRGLEV
LPLTITIGDY ILTPDICVER KSISDLIGSL NSGRLYNQCV QMQRHYAKPI LLIEFDQNKP
FHLQGKFMLS QQTSMANADI VQKLQLLTLH FPKLRLIWSP SPYATAQLFE ELKLGKPEPD
PQTAAALGSD EPTAGEQLHF NSGIYDFLLR LPGVHTRNIH GLLRKGGSLR QLLLRSQKEL
EELLQSQESA KLLYDILHVA HLPEKDEVTG STALLAASKQ FGAGSHNRFR MAAAASRRGR
R
