XRN2_DROME
ID XRN2_DROME Reviewed; 908 AA.
AC Q9VM71; B8A3W7; Q5BI90;
DT 19-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=5'-3' exoribonuclease 2 homolog;
DE EC=3.1.13.-;
DE AltName: Full=Ribonucleic acid-trafficking protein 1;
DE Short=dRAT1;
GN Name=Rat1; ORFNames=CG10354;
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley; TISSUE=Embryo;
RA Stapleton M., Carlson J.W., Booth B., Chavez C., Frise E., George R.A.,
RA Pacleb J.M., Park S., Wan K.H., Yu C., Rubin G.M., Celniker S.E.;
RL Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP IDENTIFICATION, SUBCELLULAR LOCATION, AND NO INTERACTION WITH CUFF.
RX PubMed=17363252; DOI=10.1016/j.cub.2007.02.027;
RA Chen Y., Pane A., Schuepbach T.;
RT "Cutoff and aubergine mutations result in retrotransposon upregulation and
RT checkpoint activation in Drosophila.";
RL Curr. Biol. 17:637-642(2007).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-438, 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: Possesses 5'->3' exoribonuclease activity. May promote the
CC termination of transcription by RNA polymerase II (By similarity).
CC {ECO:0000250}.
CC -!- SUBUNIT: Does not interact with cuff.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17363252}.
CC -!- SIMILARITY: Belongs to the 5'-3' exonuclease family. XRN2/RAT1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAX33482.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
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DR EMBL; AE014134; AAF52452.2; -; Genomic_DNA.
DR EMBL; BT021334; AAX33482.1; ALT_SEQ; mRNA.
DR EMBL; BT056259; ACL68706.1; -; mRNA.
DR RefSeq; NP_001260166.1; NM_001273237.1.
DR RefSeq; NP_609082.1; NM_135238.3.
DR AlphaFoldDB; Q9VM71; -.
DR SMR; Q9VM71; -.
DR BioGRID; 60115; 5.
DR IntAct; Q9VM71; 2.
DR STRING; 7227.FBpp0078973; -.
DR iPTMnet; Q9VM71; -.
DR PaxDb; Q9VM71; -.
DR PRIDE; Q9VM71; -.
DR DNASU; 33964; -.
DR EnsemblMetazoa; FBtr0079345; FBpp0078973; FBgn0031868.
DR EnsemblMetazoa; FBtr0332324; FBpp0304602; FBgn0031868.
DR GeneID; 33964; -.
DR KEGG; dme:Dmel_CG10354; -.
DR UCSC; CG10354-RA; d. melanogaster.
DR CTD; 33964; -.
DR FlyBase; FBgn0031868; Rat1.
DR VEuPathDB; VectorBase:FBgn0031868; -.
DR eggNOG; KOG2044; Eukaryota.
DR GeneTree; ENSGT00670000098098; -.
DR HOGENOM; CLU_006038_1_2_1; -.
DR InParanoid; Q9VM71; -.
DR OMA; CLHYYVH; -.
DR OrthoDB; 685597at2759; -.
DR PhylomeDB; Q9VM71; -.
DR Reactome; R-DME-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR BioGRID-ORCS; 33964; 0 hits in 1 CRISPR screen.
DR GenomeRNAi; 33964; -.
DR PRO; PR:Q9VM71; -.
DR Proteomes; UP000000803; Chromosome 2L.
DR Bgee; FBgn0031868; Expressed in cleaving embryo and 27 other tissues.
DR ExpressionAtlas; Q9VM71; baseline and differential.
DR Genevisible; Q9VM71; DM.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0008409; F:5'-3' exonuclease activity; ISS:UniProtKB.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IDA:FlyBase.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0000738; P:DNA catabolic process, exonucleolytic; ISS:UniProtKB.
DR GO; GO:0006353; P:DNA-templated transcription, termination; IEA:UniProtKB-KW.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IBA:GO_Central.
DR InterPro; IPR027073; 5_3_exoribonuclease.
DR InterPro; IPR004859; Put_53exo.
DR InterPro; IPR041412; Xrn1_helical.
DR InterPro; IPR017151; Xrn2/3/4.
DR PANTHER; PTHR12341; PTHR12341; 1.
DR Pfam; PF17846; XRN_M; 1.
DR Pfam; PF03159; XRN_N; 1.
DR PIRSF; PIRSF037239; Exonuclease_Xrn2; 1.
PE 1: Evidence at protein level;
KW Exonuclease; Hydrolase; Metal-binding; mRNA processing; Nuclease; Nucleus;
KW Phosphoprotein; Reference proteome; Transcription;
KW Transcription regulation; Transcription termination; Zinc; Zinc-finger.
FT CHAIN 1..908
FT /note="5'-3' exoribonuclease 2 homolog"
FT /id="PRO_0000249914"
FT ZN_FING 263..280
FT /note="CCHC-type"
FT REGION 409..457
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 821..908
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 409..431
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 432..456
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 438
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18327897"
SQ SEQUENCE 908 AA; 103960 MW; D9D113DB6630DD0F CRC64;
MGVPAFFRWL SRKYPSVIIE CNENKQVDAD TGRNIYEDPT LPNPNGIEFD NLYLDMNGII
HPCTHPEDKP APKNEDEMMV AIFECIDRLF GIVRPRKLLY MAIDGVAPRA KMNQQRSRRF
RAAKETTEKR LEIARIREEL LSRGCKLPPE KEKGEHFDSN CITPGTPFMD RLSKCLHYFV
HDRQNNNPAW KGIKVILSDA NVPGEGEHKI MDYIRKQRAQ PDHDPNTQHV LCGADADLIM
LGLATHEPNF TIIREEFLPN KPRPCDICNG FGHEMDKCVG LGATAPTSAN FKPDVPIGAE
VKFIFVRLSV LREYLKQTLE MPNLPFEYSF ERALDDWVFM CFFVGNDFLP HLPSLEIREG
AVDRLVELYK KCVYKTRGYL TDSGDVNLDR VQLIMTDLGN AEDQIFKSRQ RREEQFKARD
KARKRQERNQ DHGSLNQSAF GASAVGPNSQ QRSVGNYKEE AAALRNRKRT SDMANLDDED
EEENNDEVRL WEDGFKDRYY ESKFDVAPGN QQFRYAVALQ YVRGLCWVLK YYYQGCASWN
WYFPYHYAPF ASDFVNIQGL STMFEKGTKP FNPLEQLMGV FPAASSSHVP EPWAKLMSDP
ESPIIDFYPE DFKIDLNGKK FAWQGVALLP FVDEKRLFKA LVPYYDQLTG EEVKRNKRGD
NYLYISNQSP HYKKVKKISE KDDESVCKAI SFDGMRGTLG KTELNTAISG VLKSPISGLS
DINDNITVTT TFRDPEYDED YIFEAKRLEN AVDPPQVLPN EQSGNKHRPV IGFNSHLTRA
YVPDSGHRML NAGIRNQQGG GGNGGGGGGY GQGGGYGQGI GGNQGQSYQN NSRNYNYNYN
NNYNQHQGGG YQNNYNNRQQ QQYGHNQRFN QDNSNQQQRN FNNYNGPRNN NYQQQGGSRQ
QNQNYRRF
