DICER_DANRE
ID DICER_DANRE Reviewed; 1865 AA.
AC Q6TV19;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 2.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Endoribonuclease Dicer;
DE EC=3.1.26.3;
GN Name=dicer1;
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;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
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 [2]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 612-1865.
RX PubMed=14528306; DOI=10.1038/ng1251;
RA Wienholds E., Koudijs M.J., van Eeden F.J.M., Cuppen E., Plasterk R.H.A.;
RT "The microRNA-producing enzyme Dicer1 is essential for zebrafish
RT development.";
RL Nat. Genet. 35:217-218(2003).
CC -!- FUNCTION: Double-stranded RNA (dsRNA) endoribonuclease playing a
CC central role in short dsRNA-mediated post-transcriptional gene
CC silencing. Cleaves naturally occurring long dsRNAs and short hairpin
CC pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three
CC nucleotides with 3' overhang of two nucleotides, producing respectively
CC short interfering RNAs (siRNA) and mature microRNAs. SiRNAs and miRNAs
CC serve as guide to direct the RNA-induced silencing complex (RISC) to
CC complementary RNAs to degrade them or prevent their translation. Gene
CC silencing mediated by siRNAs, also called RNA interference, controls
CC the elimination of transcripts from mobile and repetitive DNA elements
CC of the genome but also the degradation of exogenous RNA of viral origin
CC for instance. The miRNA pathway on the other side is a mean to
CC specifically regulate the expression of target genes (By similarity).
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.3;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium or manganese ions per subunit. {ECO:0000250};
CC -!- SUBUNIT: Component of the RISC loading complex (RLC), or micro-RNA
CC (miRNA) loading complex (miRLC), which is composed of dicer1, ago2 and
CC tarbp2; dicer1 and tarbp2 are required to process precursor miRNAs
CC (pre-miRNAs) to mature miRNAs and then load them onto ago2. Note that
CC the trimeric RLC/miRLC is also referred to as RISC (By similarity).
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00657}.
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DR EMBL; AL772219; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AY386319; AAQ90464.1; -; mRNA.
DR RefSeq; NP_001154925.1; NM_001161453.2.
DR RefSeq; XP_005158722.1; XM_005158665.3.
DR RefSeq; XP_005158723.1; XM_005158666.3.
DR AlphaFoldDB; Q6TV19; -.
DR SMR; Q6TV19; -.
DR STRING; 7955.ENSDARP00000045880; -.
DR PaxDb; Q6TV19; -.
DR PRIDE; Q6TV19; -.
DR Ensembl; ENSDART00000045881; ENSDARP00000045880; ENSDARG00000001129.
DR GeneID; 324724; -.
DR KEGG; dre:324724; -.
DR CTD; 23405; -.
DR ZFIN; ZDB-GENE-030131-3445; dicer1.
DR eggNOG; KOG0701; Eukaryota.
DR GeneTree; ENSGT00940000156287; -.
DR HOGENOM; CLU_000907_4_4_1; -.
DR InParanoid; Q6TV19; -.
DR OMA; TTYLYCT; -.
DR OrthoDB; 1337630at2759; -.
DR PhylomeDB; Q6TV19; -.
DR TreeFam; TF330258; -.
DR Reactome; R-DRE-203927; MicroRNA (miRNA) biogenesis.
DR Reactome; R-DRE-426486; Small interfering RNA (siRNA) biogenesis.
DR PRO; PR:Q6TV19; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 17.
DR Bgee; ENSDARG00000001129; Expressed in cardiac ventricle and 26 other tissues.
DR ExpressionAtlas; Q6TV19; baseline.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0016442; C:RISC complex; ISS:UniProtKB.
DR GO; GO:0070578; C:RISC-loading complex; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004530; F:deoxyribonuclease I activity; IBA:GO_Central.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0070883; F:pre-miRNA binding; IDA:ZFIN.
DR GO; GO:0004525; F:ribonuclease III activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0006309; P:apoptotic DNA fragmentation; IBA:GO_Central.
DR GO; GO:1904888; P:cranial skeletal system development; IMP:ZFIN.
DR GO; GO:0098795; P:global gene silencing by mRNA cleavage; ISS:UniProtKB.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:ZFIN.
DR GO; GO:0030318; P:melanocyte differentiation; IMP:ZFIN.
DR GO; GO:0035196; P:miRNA processing; IMP:ZFIN.
DR GO; GO:0035195; P:miRNA-mediated gene silencing; IMP:ZFIN.
DR GO; GO:0035279; P:miRNA-mediated gene silencing by mRNA destabilization; IGI:ZFIN.
DR GO; GO:0014032; P:neural crest cell development; IMP:ZFIN.
DR GO; GO:0031054; P:pre-miRNA processing; IDA:ZFIN.
DR GO; GO:0050767; P:regulation of neurogenesis; IMP:ZFIN.
DR GO; GO:0090501; P:RNA phosphodiester bond hydrolysis; IBA:GO_Central.
DR GO; GO:0030422; P:siRNA processing; ISS:UniProtKB.
DR GO; GO:0021591; P:ventricular system development; IMP:ZFIN.
DR CDD; cd10843; DSRM_DICER; 1.
DR CDD; cd00593; RIBOc; 2.
DR Gene3D; 1.10.1520.10; -; 2.
DR Gene3D; 3.30.160.380; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR038248; Dicer_dimer_sf.
DR InterPro; IPR005034; Dicer_dimerisation_dom.
DR InterPro; IPR044441; DICER_DSRM.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR003100; PAZ_dom.
DR InterPro; IPR036085; PAZ_dom_sf.
DR InterPro; IPR000999; RNase_III_dom.
DR InterPro; IPR036389; RNase_III_sf.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF02170; PAZ; 1.
DR Pfam; PF00636; Ribonuclease_3; 2.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00358; DSRM; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00949; PAZ; 1.
DR SMART; SM00535; RIBOc; 2.
DR SUPFAM; SSF101690; SSF101690; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF69065; SSF69065; 2.
DR PROSITE; PS51327; DICER_DSRBF; 1.
DR PROSITE; PS50137; DS_RBD; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS50821; PAZ; 1.
DR PROSITE; PS00517; RNASE_3_1; 1.
DR PROSITE; PS50142; RNASE_3_2; 2.
PE 2: Evidence at transcript level;
KW ATP-binding; Cytoplasm; Endonuclease; Helicase; Hydrolase; Magnesium;
KW Manganese; Metal-binding; Nuclease; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Repeat; RNA-binding; RNA-mediated gene silencing.
FT CHAIN 1..1865
FT /note="Endoribonuclease Dicer"
FT /id="PRO_0000373985"
FT DOMAIN 41..213
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 419..588
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 616..708
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 877..1028
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 1262..1385
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1609..1767
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1792..1857
FT /note="DRBM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 397..417
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 713..732
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1111..1142
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1190..1259
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1373..1417
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 161..164
FT /note="DECH box"
FT COMPBIAS 398..412
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1113..1132
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1190..1204
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1221..1237
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1238..1257
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1375..1392
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1393..1417
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 54..61
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1298
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1377
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1380
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1648
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 1753
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 1756
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT SITE 1749
FT /note="Important for activity"
FT /evidence="ECO:0000250"
FT CONFLICT 739..751
FT /note="IPECLRGCYPVPE -> VK (in Ref. 2; AAQ90464)"
FT /evidence="ECO:0000305"
FT CONFLICT 921
FT /note="R -> K (in Ref. 2; AAQ90464)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1865 AA; 210817 MW; 55B1700E719B2007 CRC64;
MAGLQLVTPA SSPMGPFFGL PWQQEAIHDN IYTPRKYQVE LLEAALEHNT IVCLNTGSGK
TFIAVLLIKE LSHQIRGENG KRTVFLVNAA SSVAQQASTV RTHSDLQVGD YMSEDMTSWP
EEMWNREMIE NQVLVMTCHI FLHVLKNGVL PLSKINLLVF DECHLAITGH PYREIMKICE
GCPSCPRILG LTASILNGKC DPCDLEEKIQ NLEKILQSNA ETATDLVVLD RYASQPREEV
LDCGQYQDQS GLSERLLNEL DEALNFLNDC NLSVHREDRD PTFISKQVLN DCRAVLTVLG
PWCADKAAGI MVRELQKYIK HEQEELNRKF LLFTDTILRK IHALCEEHFS PASLDLKFVT
PKVIRLLEIL HEYKPFERQQ FESVEWYNNR NQDNYVSWSD SEDDDEDEEA EAKEKTEANF
PSPFTNILCG IIFVERRYTA VVLNRLIKEA GKQDPELAYI SSNFITGHSI GKNQPRNKQM
EVEFRKQEEV LRKFRAHETN LLIATSIVEE GVDIPKCNLV VRFDLPTEYR SYVQSKGRAR
APVSNYIMLA DSERTKTFQE DLKTYKAIEK ILRNKCSKSA ECNDFELEPV TDDDNVLPPY
VLRSEDGGPR VTMNTAIGHV NRYCARLPSD PFTHLAPKCK TVEMNTGGYR STLFLPINSP
LRVPVTGPVM NCARLAEKAV ALLCCEKLHK IGELDDHLMP VGKETVKYEE ELDLHDEEET
SVPGRPGSTK RRQCSPKAIP ECLRGCYPVP EQPCYLYVIG MVLTTPLPDE LNFRRRKLYP
PEDTTRCFGI LTAKPIPRIP HFPVYTRSGE VTISIELQKS GFSLSAEQLE LITRLHQYIF
SHILRLEKPA LEFKPVEADS AYCVLPLNIV EDSNTLDLDF KFMEDIEKSE ARIGIPNTQY
TKQNPFIFKL EDYQDAVIIP RYRNFDQPHR FYVADVYTDL TPLSKFPSPE YETFAEYYKT
KYNLDLSNVN QPLLDVDHTS SRLNLLTPRH LNQKGKALPL SSAEKRKAKW ESLQNKQILV
PELCAIHPIP ASLWRKAVCL PSILYRLHCL LTAEELRSQT AIDAGVGAQT LPPDFRYPNL
DFGWKKSIDS KSFISCPSAC MEEDDDHCKL GTSSDSNHTA PESCSMEVSQ PPEGAPNTPD
EKLETLTLPV TDLNKDCFPN LPNGTQADSD DLPHRSDVCQ CSQLGPLERD LSTQTTTSVS
VRPSPAGEPQ PWPSDECTGR SSDLCDPHVK KPTSKHCPKS ETATSTPAPS ETSSEDCRSA
CAGPAWDSPK TLGPNPGLIL QALTLSNASD GFNLERLEML GDSFLKHAIT TYLFCTYPDA
HEGRLSYMRS KKVSNCNLYR LGKKKGLPSR MVVSIFDPPV NWLPPGYVVN QDKSSTDKWD
SDENKDLANG KASDDEDEDD DDEPEEAEVE PSKEDVNVED DLEYYYEHIR FIDSMLIGSG
AFGKKISLQP TDPGYEWKAP KKAHNSHFSP DGGADEFDYS SWDAMCYLDP SKAGEEDDFV
VGFWNPSEEN CGTDIGKQSI SYDLHTEQCI ADKSIADCVE ALLGCYLTSC GERAAQLFLC
SLGLKVLPPE KQSSGGSAEL QYGWLKIPPR CMFEHPDAER TLNHLISGFL NFESKINYTF
KNKAYLLQAF THASYHYNTI TDCYQRLEFL GDAILDYLIT KHLYEDPRQH SPGVLTDLRS
ALVNNTIFAS LAVKYDYHKY FKAVSPELFH VIDDFVQFQL EKNEMQGMDS ELRRSEEDEE
KEEDIEVPKA MGDIFESLAG AIYMDSGMSL ETVWQVYYPM MRPLIEKFSA NVPRSPVREL
LEMEPETAKF SPAERTYDGK VRVTVEVVGK GKFKGVGRSY RIAKSAAARR ALRSLKANQP
QVQNN
