RENT1_DANRE
ID RENT1_DANRE Reviewed; 1100 AA.
AC F1RCY6; A0A0R4IY20; Q7ZVZ4;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=Regulator of nonsense transcripts 1 {ECO:0000250|UniProtKB:Q92900};
DE EC=3.6.4.-;
DE AltName: Full=ATP-dependent helicase RENT1 {ECO:0000250|UniProtKB:Q9EPU0};
DE AltName: Full=Nonsense mRNA reducing factor 1 {ECO:0000250|UniProtKB:Q92900};
DE Short=NORF1 {ECO:0000250|UniProtKB:Q92900};
DE AltName: Full=Up-frameshift suppressor 1 homolog {ECO:0000250|UniProtKB:Q92900};
GN Name=upf1 {ECO:0000312|ZFIN:ZDB-GENE-040426-2836};
GN Synonyms=rent1 {ECO:0000312|ZFIN:ZDB-GENE-040426-2836};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000312|Proteomes:UP000000437};
RN [1] {ECO:0000312|EMBL:CAX18770.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=19414594; DOI=10.1128/mcb.00177-09;
RA Wittkopp N., Huntzinger E., Weiler C., Sauliere J., Schmidt S.,
RA Sonawane M., Izaurralde E.;
RT "Nonsense-mediated mRNA decay effectors are essential for zebrafish
RT embryonic development and survival.";
RL Mol. Cell. Biol. 29:3517-3528(2009).
RN [2] {ECO:0000312|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000312|Proteomes:UP000000437};
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3] {ECO:0000312|EMBL:AAH45353.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=AB {ECO:0000312|EMBL:AAH45353.1};
RC TISSUE=Embryo {ECO:0000312|EMBL:AAH45353.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000305}
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=21227923; DOI=10.1093/nar/gkq1319;
RA Anastasaki C., Longman D., Capper A., Patton E.E., Caceres J.F.;
RT "Dhx34 and Nbas function in the NMD pathway and are required for embryonic
RT development in zebrafish.";
RL Nucleic Acids Res. 39:3686-3694(2011).
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.
CC {ECO:0000250|UniProtKB:Q92900}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q9EPU0}.
CC Cytoplasm, P-body {ECO:0000250|UniProtKB:Q92900}. Nucleus
CC {ECO:0000250|UniProtKB:Q92900}. Cytoplasm, perinuclear region
CC {ECO:0000250|UniProtKB:Q9EPU0}.
CC -!- DEVELOPMENTAL STAGE: Expressed during early cleavage, gastrulation and
CC at 1 day post-fertilization. {ECO:0000269|PubMed:19414594}.
CC -!- DISRUPTION PHENOTYPE: Morpholino knockdown leads to both intermediate
CC and severe phenotypes of abnormal embryonic development
CC (PubMed:21227923, PubMed:19414594). Intermediate phenotypes show
CC developmental delay, including aberrant formation of the head, tail,
CC eye placodes and somites (PubMed:21227923, PubMed:19414594). Severe
CC phenotypes show severe developmental arrest, including yolk extension
CC defects, and lack of recognizable morphological development
CC (PubMed:21227923, PubMed:19414594). High mortality rates of 80% to 85%
CC at 5 days post-fertilization (PubMed:19414594). Increase in premature
CC stop codon containing slc24a5 mRNA transcript levels in melanocytes
CC (PubMed:21227923, PubMed:19414594). {ECO:0000269|PubMed:19414594,
CC ECO:0000269|PubMed:21227923}.
CC -!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family.
CC {ECO:0000250|UniProtKB:Q92900}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; FM986817; CAX18770.1; -; mRNA.
DR EMBL; CR931779; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CU693375; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC045353; AAH45353.1; -; mRNA.
DR RefSeq; NP_998639.1; NM_213474.1.
DR AlphaFoldDB; F1RCY6; -.
DR SMR; F1RCY6; -.
DR STRING; 7955.ENSDARP00000013006; -.
DR PaxDb; F1RCY6; -.
DR Ensembl; ENSDART00000021011; ENSDARP00000013006; ENSDARG00000016302.
DR Ensembl; ENSDART00000180271; ENSDARP00000153550; ENSDARG00000016302.
DR GeneID; 406783; -.
DR KEGG; dre:406783; -.
DR CTD; 5976; -.
DR ZFIN; ZDB-GENE-040426-2836; upf1.
DR eggNOG; KOG1802; Eukaryota.
DR GeneTree; ENSGT00940000157413; -.
DR HOGENOM; CLU_001666_4_3_1; -.
DR InParanoid; F1RCY6; -.
DR OMA; TDRGQHG; -.
DR OrthoDB; 62494at2759; -.
DR PhylomeDB; F1RCY6; -.
DR TreeFam; TF300554; -.
DR Reactome; R-DRE-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
DR Reactome; R-DRE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 2.
DR Bgee; ENSDARG00000016302; Expressed in pharyngeal gill and 28 other tissues.
DR ExpressionAtlas; F1RCY6; baseline.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000932; C:P-body; IEA:UniProtKB-SubCell.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
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:0043009; P:chordate embryonic development; IMP:UniProtKB.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IMP:UniProtKB.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:UniProtKB.
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 2: Evidence at transcript level;
KW ATP-binding; Cytoplasm; Helicase; Hydrolase; Metal-binding; Methylation;
KW Nonsense-mediated mRNA decay; Nucleotide-binding; Nucleus;
KW Reference proteome; RNA-binding; Zinc; Zinc-finger.
FT CHAIN 1..1100
FT /note="Regulator of nonsense transcripts 1"
FT /id="PRO_0000454185"
FT DOMAIN 94..251
FT /note="Upf1 CH-rich"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 42..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 102..134
FT /note="C3H"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 116..144
FT /note="CC/SHH/C"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 162..192
FT /note="C4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 978..1065
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 42..60
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1005..1065
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 102
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 105
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 116
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 119
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 124
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 134
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 138
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 144
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 165
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 188
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 192
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 455
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 475..479
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 645
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 682
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"
FT CONFLICT 96
FT /note="D -> V (in Ref. 1; CAX18770 and 3; AAH45353)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1100 AA; 122079 MW; 4DEA014222AA8F59 CRC64;
MSVEAYGPSS QTLTFLDTEE AELLGADTQG SEFEFTDFTL PSQTQTQGQT QSQLDNQVNG
PDGVLPNGED AVGKTSQLLA ELNFEEDEED TYYTKDLPVH ACSYCGIHDP ACVVYCNTSK
KWFCNGRGNT SGSHIVNHLV RAKCKEVTLH KDGPLGETVL ECYNCGCRNV FLLGFIPAKA
DSVVVLLCRQ PCASQSSLKD INWDSSQWQP LIQDRCFLSW LVKIPSEQEQ LRARQITAQQ
INKLEELWKE NPTATLEDLE KPGVDEEPQH VLLRYEDAYQ YQNIFGPLVK LEADYDKKLK
ESQTQDNITV RWDLGLNKKR IAYFTLPKTD SGDMRLMQGD EICLRYKGDM APLWKGIGHV
IKVPDNYGDE IAIELRSSAG APVEVPHNFQ VDFVWKSTSF DRMQSALKTF AVDETSVSGY
IYHKLLGHEV EDVIIKCQLP KRFTAQGLPD LNHSQVYAVK TVLQRPLSLI QGPPGTGKTV
TSATIVYHLA RQGNGPVLVC APSNIAVDQL TEKIHQTGLK VVRLCAKSRE AIDSPVSFLA
LHNQIRNMDS MPELQKLQQL KDETGELSSS DEKRYRALKR TAERELLMNA DVICCTCVGA
GDPRLAKMQF RSILIDESTQ ATEPECMVPV VLGAKQLILV GDHCQLGPVV MCKKAAKAGL
SQSLFERLVV LGIRPIRLQV QYRMHPALSA FPSNIFYEGS LQNGVTAADR LKKGFDFQWP
QPDKPMFFYV TQGQEEIASS GTSYLNRTEA ANVEKITTRL LKAGAKPDQI GIITPYEGQR
SYLVQYMQFS GSLHTKLYQE VEIASVDAFQ GREKDFIILS CVRANEHQGI GFLNDPRRLN
VALTRARYGV IIVGNPKALS KQPLWNHLLN YYKEQKVLVE GPLNNLRESL MQFSKPRKLV
NTINPGARFM STAMYDAREA MIPGSVYDRS STGRPSNMYF QTHDQVGMIG TGPNPMGSLN
IPIPFNLVMP PMPPPGYLGQ VNGPAAGRGA PKGKTGGRGG RQRNRGTGNH GSGQPNMPNS
QASQDLVSQP FSQGPLTQGY ITMSQPSQMS QPGLSQPELS QDSYLGDEFK SQMDVALSQD
STYQGERAYQ HGGVTGLSQY
