RENT1_DROME
ID RENT1_DROME Reviewed; 1180 AA.
AC Q9VYS3; Q95RG9;
DT 18-OCT-2001, integrated into UniProtKB/Swiss-Prot.
DT 27-JAN-2003, sequence version 2.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Regulator of nonsense transcripts 1 homolog;
DE EC=3.6.4.12 {ECO:0000250|UniProtKB:Q92900};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:Q92900};
GN Name=Upf1; ORFNames=CG1559;
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;
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 [4]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=12881430; DOI=10.1093/emboj/cdg371;
RA Gatfield D., Ciccarelli F.D., Bork P., Izaurralde E.;
RT "Nonsense-mediated mRNA decay in Drosophila: at the intersection of the
RT yeast and mammalian pathways.";
RL EMBO J. 22:3960-3970(2003).
RN [5]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=16199763; DOI=10.1261/rna.2160905;
RA Rehwinkel J., Letunic I., Raes J., Bork P., Izaurralde E.;
RT "Nonsense-mediated mRNA decay factors act in concert to regulate common
RT mRNA targets.";
RL RNA 11:1530-1544(2005).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=17178403; DOI=10.1016/j.neuron.2006.10.028;
RA Barbee S.A., Estes P.S., Cziko A.M., Hillebrand J., Luedeman R.A.,
RA Coller J.M., Johnson N., Howlett I.C., Geng C., Ueda R., Brand A.H.,
RA Newbury S.F., Wilhelm J.E., Levine R.B., Nakamura A., Parker R.,
RA Ramaswami M.;
RT "Staufen- and FMRP-containing neuronal RNPs are structurally and
RT functionally related to somatic P bodies.";
RL Neuron 52:997-1009(2006).
CC -!- FUNCTION: RNA-dependent helicase and ATPase required for nonsense-
CC mediated decay (NMD) of mRNAs containing premature stop codons. Is
CC recruited to mRNAs upon translation termination and undergoes a cycle
CC of phosphorylation and dephosphorylation; its phosphorylation appears
CC to be a key step in NMD. The formation of an Upf1-Upf2-Upf3
CC surveillance complex is believed to activate NMD (By similarity).
CC {ECO:0000250|UniProtKB:Q92900, ECO:0000269|PubMed:12881430,
CC ECO:0000269|PubMed:16199763}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13066;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13066;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:17178403}.
CC Cytoplasm, Cytoplasmic ribonucleoprotein granule
CC {ECO:0000269|PubMed:17178403}.
CC -!- PTM: Phosphorylated, probably by nonC. {ECO:0000305|PubMed:12881430,
CC ECO:0000305|PubMed:16199763}.
CC -!- MISCELLANEOUS: In Drosophila, the definition of premature stop codons
CC in mRNAs appears to be independent of exon boundaries and of the EJC
CC complex.
CC -!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family. {ECO:0000305}.
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DR EMBL; AE014298; AAF48115.2; -; Genomic_DNA.
DR EMBL; AY061379; AAL28927.1; -; mRNA.
DR RefSeq; NP_001285145.1; NM_001298216.1.
DR RefSeq; NP_572767.1; NM_132539.3.
DR AlphaFoldDB; Q9VYS3; -.
DR SMR; Q9VYS3; -.
DR BioGRID; 58558; 7.
DR IntAct; Q9VYS3; 10.
DR STRING; 7227.FBpp0073433; -.
DR PaxDb; Q9VYS3; -.
DR PRIDE; Q9VYS3; -.
DR DNASU; 32153; -.
DR EnsemblMetazoa; FBtr0073596; FBpp0073433; FBgn0030354.
DR EnsemblMetazoa; FBtr0342744; FBpp0309612; FBgn0030354.
DR GeneID; 32153; -.
DR KEGG; dme:Dmel_CG1559; -.
DR UCSC; CG1559-RA; d. melanogaster.
DR CTD; 5976; -.
DR FlyBase; FBgn0030354; Upf1.
DR VEuPathDB; VectorBase:FBgn0030354; -.
DR eggNOG; KOG1802; Eukaryota.
DR HOGENOM; CLU_001666_4_3_1; -.
DR InParanoid; Q9VYS3; -.
DR OMA; HHDSIGY; -.
DR OrthoDB; 62494at2759; -.
DR PhylomeDB; Q9VYS3; -.
DR Reactome; R-DME-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
DR Reactome; R-DME-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR SignaLink; Q9VYS3; -.
DR BioGRID-ORCS; 32153; 1 hit in 1 CRISPR screen.
DR GenomeRNAi; 32153; -.
DR PRO; PR:Q9VYS3; -.
DR Proteomes; UP000000803; Chromosome X.
DR Bgee; FBgn0030354; Expressed in eye disc (Drosophila) and 22 other tissues.
DR ExpressionAtlas; Q9VYS3; baseline and differential.
DR Genevisible; Q9VYS3; DM.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:1990124; C:messenger ribonucleoprotein complex; IDA:UniProtKB.
DR GO; GO:0071598; C:neuronal ribonucleoprotein granule; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0036121; F:double-stranded DNA helicase activity; ISS:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0071456; P:cellular response to hypoxia; IMP:FlyBase.
DR GO; GO:0032508; P:DNA duplex unwinding; ISS:UniProtKB.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:FlyBase.
DR GO; GO:2000624; P:positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:FlyBase.
DR CDD; cd21407; 1B_UPF1-like; 1.
DR CDD; cd18808; SF1_C_Upf1; 1.
DR CDD; cd21400; ZBD_UPF1-like; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR045055; DNA2/NAM7-like.
DR InterPro; IPR041679; DNA2/NAM7-like_C.
DR InterPro; IPR041677; DNA2/NAM7_AAA_11.
DR InterPro; IPR006935; Helicase/UvrB_N.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR040812; UPF1_1B_dom.
DR InterPro; IPR018999; UPF1_CH/ZBD.
DR PANTHER; PTHR10887; PTHR10887; 1.
DR Pfam; PF13086; AAA_11; 1.
DR Pfam; PF13087; AAA_12; 1.
DR Pfam; PF04851; ResIII; 1.
DR Pfam; PF18141; UPF1_1B_dom; 1.
DR Pfam; PF09416; UPF1_Zn_bind; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51997; UPF1_CH_RICH; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Helicase; Hydrolase; Metal-binding;
KW Nucleotide-binding; Phosphoprotein; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..1180
FT /note="Regulator of nonsense transcripts 1 homolog"
FT /id="PRO_0000080720"
FT DOMAIN 92..249
FT /note="Upf1 CH-rich"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 21..51
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 100..132
FT /note="C3H"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 114..142
FT /note="CC/SHH/C"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 160..190
FT /note="C4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 1062..1110
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 32..51
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1084..1110
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 100
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 114
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 117
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 122
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 132
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 136
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 160
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 163
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 186
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 190
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 456
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 473..480
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00499"
FT BINDING 646
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 683
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 813
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
SQ SEQUENCE 1180 AA; 129913 MW; 150EAA970D221D0E CRC64;
MSVDTYAPSS ALSFLDMDDN ELLPGADTQP TQYDYRDFTM PSTSQSQTQN DQLEIAQRCS
AGDSHPRLAS ITNDLADLQF EEEDDEPGSS YVKELPPHAC KYCGIHDPAT VVMCNNCRKW
FCNGRGSTSG SHIINHLVRA KHREVTLHGE GPLGETILEC YSCGVRNVFV LGFIPAKADS
VVVLLCRQPC AAQNSLKDMN WDQEQWKPLI ADRCFLAWLV KQPSEQGQLR ARQISAAQIN
KLEELWKENI EATFQDLEKP GIDSEPAHVL LRYEDGYQYE KTFGPLVRLE AEYDQKLKES
ATQENIEVRW DVGLNKKTIA YFTLAKTDSD MKLMHGDELR LHYVGELYNP WSEIGHVIKV
PDNFGDDVGL ELKSSTNAPV KCTSNFTVDF IWKCTSFDRM TRALCKFAID RNSVSNFIYS
RLLGHGRADS NDEVLFRGPQ PKLFSAPHLP DLNRSQVYAV KHALQRPLSL IQGPPGTGKT
VTSATIVYQL VKLHGGTVLV CAPSNTAVDQ LTEKIHRTNL KVVRVCAKSR EAIDSPVSFL
ALHNQIRNME TNSELKKLQQ LKDETGELSS ADEKRYRNLK RAAENQLLEA ADVICCTCVG
AGDGRLSRVK FTSILIDESM QSTEPECMVP VVLGAKQLIL VGDHCQLGPV VMCKKAARAG
LSQSLFERLV VLGIRPFRLE VQYRMHPELS QFPSNFFYEG SLQNGVCAED RRLKLDFPWP
QPERPMFFLV TQGQEEIAGS GTSFLNRTEA ANVEKITTRF LKAGIKPEQI GIITPYEGQR
AYLVQYMQYQ GSLHSRLYQE IEIASVDAFQ GREKDIIIMS CVRSNERQGI GFLNDPRRLN
VALTRAKFGI IIVGNPKVLA KQQLWNHLLN FYKDRKVLVE GSLNNLKESL IHFQKPKKLV
NSMNIGAHFM STIIADAKEV MVPGSIYDRS GGYGQGRQMV GQSMNGGQYG GSGGGPYGNS
PLGYGTPSSN SMVGFGLGNG GNGAAGGNNN FGGAGPSWAA AHLHHDSIGY ISNEHGAAAL
GNMPVPVGMF MNMSNIPPRF YNQHQQAIMA VKQNRAIQQQ TGNFSPGNSG PGVTGVGVGR
SATPGGNKKT NKLGKSRVTG GGTGGAPLTQ GSSVCNAAPY SQHPMPLSLQ MTQPSGFALS
QQPELSQDFG QISQMDGLLS QDVAFNASGE RSLNQFSQPY
