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Endoribonuclease Dicer (EC 3.1.26.3)

 DICER_DANRE             Reviewed;        1865 AA.
Q6TV19;
05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
05-MAY-2009, sequence version 2.
28-MAR-2018, entry version 93.
RecName: Full=Endoribonuclease Dicer;
EC=3.1.26.3;
Name=dicer1;
Danio rerio (Zebrafish) (Brachydanio rerio).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
Cyprinidae; Danio.
NCBI_TaxID=7955;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Tuebingen;
PubMed=23594743; DOI=10.1038/nature12111;
Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C.,
Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L.,
McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C.,
Koch R., Rauch G.J., White S., Chow W., Kilian B., Quintais L.T.,
Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T.,
Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F.,
Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H.,
Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G.,
Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B.,
Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S.,
Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C.,
Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H.,
Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C.,
Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
Humphries M., Sycamore N., Barker D., Saunders D., Wallis J.,
Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S.,
Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R.,
Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R.,
Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R.,
Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A.,
Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S.,
Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J.,
Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C.,
Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H.,
Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J.,
Stemple D.L.;
"The zebrafish reference genome sequence and its relationship to the
human genome.";
Nature 496:498-503(2013).
[2]
NUCLEOTIDE SEQUENCE [MRNA] OF 612-1865.
PubMed=14528306; DOI=10.1038/ng1251;
Wienholds E., Koudijs M.J., van Eeden F.J.M., Cuppen E.,
Plasterk R.H.A.;
"The microRNA-producing enzyme Dicer1 is essential for zebrafish
development.";
Nat. Genet. 35:217-218(2003).
-!- FUNCTION: Double-stranded RNA (dsRNA) endoribonuclease playing a
central role in short dsRNA-mediated post-transcriptional gene
silencing. Cleaves naturally occurring long dsRNAs and short
hairpin pre-microRNAs (miRNA) into fragments of twenty-one to
twenty-three nucleotides with 3' overhang of two nucleotides,
producing respectively short interfering RNAs (siRNA) and mature
microRNAs. SiRNAs and miRNAs serve as guide to direct the RNA-
induced silencing complex (RISC) to complementary RNAs to degrade
them or prevent their translation. Gene silencing mediated by
siRNAs, also called RNA interference, controls the elimination of
transcripts from mobile and repetitive DNA elements of the genome
but also the degradation of exogenous RNA of viral origin for
instance. The miRNA pathway on the other side is a mean to
specifically regulate the expression of target genes (By
similarity). {ECO:0000250}.
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage to 5'-
phosphomonoester.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Binds 2 magnesium or manganese ions per subunit.
{ECO:0000250};
-!- SUBUNIT: Component of the RISC loading complex (RLC), or micro-RNA
(miRNA) loading complex (miRLC), which is composed of dicer1, ago2
and tarbp2; dicer1 and tarbp2 are required to process precursor
miRNAs (pre-miRNAs) to mature miRNAs and then load them onto ago2.
Note that the trimeric RLC/miRLC is also referred to as RISC (By
similarity). {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
-!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
{ECO:0000255|PROSITE-ProRule:PRU00657}.
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EMBL; AL772219; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AY386319; AAQ90464.1; -; mRNA.
RefSeq; NP_001154925.1; NM_001161453.2.
RefSeq; XP_005158722.1; XM_005158665.3.
RefSeq; XP_005158723.1; XM_005158666.3.
UniGene; Dr.78137; -.
SMR; Q6TV19; -.
STRING; 7955.ENSDARP00000045880; -.
PaxDb; Q6TV19; -.
Ensembl; ENSDART00000045881; ENSDARP00000045880; ENSDARG00000001129.
Ensembl; ENSDART00000109826; ENSDARP00000100328; ENSDARG00000001129.
GeneID; 324724; -.
KEGG; dre:324724; -.
CTD; 23405; -.
ZFIN; ZDB-GENE-030131-3445; dicer1.
eggNOG; KOG0701; Eukaryota.
eggNOG; COG0571; LUCA.
eggNOG; COG1111; LUCA.
GeneTree; ENSGT00510000046789; -.
HOGENOM; HOG000001567; -.
InParanoid; Q6TV19; -.
KO; K11592; -.
OMA; CYPKAIP; -.
PhylomeDB; Q6TV19; -.
TreeFam; TF330258; -.
Reactome; R-DRE-203927; MicroRNA (miRNA) biogenesis.
Reactome; R-DRE-426486; Small interfering RNA (siRNA) biogenesis.
PRO; PR:Q6TV19; -.
Proteomes; UP000000437; Chromosome 17.
Bgee; ENSDARG00000001129; -.
ExpressionAtlas; Q6TV19; baseline.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0035068; C:micro-ribonucleoprotein complex; ISS:UniProtKB.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0016442; C:RISC complex; IBA:GO_Central.
GO; GO:0070578; C:RISC-loading complex; ISS:UniProtKB.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004530; F:deoxyribonuclease I activity; IBA:GO_Central.
GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0070883; F:pre-miRNA binding; IDA:ZFIN.
GO; GO:0004525; F:ribonuclease III activity; IBA:GO_Central.
GO; GO:0006309; P:apoptotic DNA fragmentation; IBA:GO_Central.
GO; GO:0035195; P:gene silencing by miRNA; IMP:ZFIN.
GO; GO:0035279; P:mRNA cleavage involved in gene silencing by miRNA; IGI:ZFIN.
GO; GO:0031054; P:pre-miRNA processing; IMP:ZFIN.
GO; GO:0035196; P:production of miRNAs involved in gene silencing by miRNA; IMP:ZFIN.
GO; GO:0030422; P:production of siRNA involved in RNA interference; ISS:UniProtKB.
GO; GO:0050767; P:regulation of neurogenesis; IMP:ZFIN.
GO; GO:0030423; P:targeting of mRNA for destruction involved in RNA interference; ISS:UniProtKB.
GO; GO:0021591; P:ventricular system development; IMP:ZFIN.
CDD; cd00079; HELICc; 1.
CDD; cd00593; RIBOc; 2.
Gene3D; 1.10.1520.10; -; 1.
Gene3D; 3.30.160.380; -; 1.
InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
InterPro; IPR038248; Dicer_dimer_sf.
InterPro; IPR005034; Dicer_dimerisation_dom.
InterPro; IPR014720; dsRBD_dom.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR003100; PAZ_dom.
InterPro; IPR036085; PAZ_dom_sf.
InterPro; IPR000999; RNase_III_dom.
InterPro; IPR036389; RNase_III_sf.
Pfam; PF00270; DEAD; 1.
Pfam; PF03368; Dicer_dimer; 1.
Pfam; PF00271; Helicase_C; 1.
Pfam; PF02170; PAZ; 1.
Pfam; PF00636; Ribonuclease_3; 2.
SMART; SM00487; DEXDc; 1.
SMART; SM00358; DSRM; 1.
SMART; SM00490; HELICc; 1.
SMART; SM00949; PAZ; 1.
SMART; SM00535; RIBOc; 2.
SUPFAM; SSF101690; SSF101690; 1.
SUPFAM; SSF52540; SSF52540; 3.
SUPFAM; SSF69065; SSF69065; 4.
PROSITE; PS51327; DICER_DSRBF; 1.
PROSITE; PS50137; DS_RBD; 1.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
PROSITE; PS50821; PAZ; 1.
PROSITE; PS00517; RNASE_3_1; 1.
PROSITE; PS50142; RNASE_3_2; 2.
2: Evidence at transcript level;
ATP-binding; Complete proteome; Cytoplasm; Endonuclease; Helicase;
Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease;
Nucleotide-binding; Phosphoprotein; Reference proteome; Repeat;
RNA-binding; RNA-mediated gene silencing.
CHAIN 1 1865 Endoribonuclease Dicer.
/FTId=PRO_0000373985.
DOMAIN 41 213 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 419 588 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
DOMAIN 616 708 Dicer dsRNA-binding fold.
{ECO:0000255|PROSITE-ProRule:PRU00657}.
DOMAIN 877 1028 PAZ. {ECO:0000255|PROSITE-
ProRule:PRU00142}.
DOMAIN 1262 1385 RNase III 1. {ECO:0000255|PROSITE-
ProRule:PRU00177}.
DOMAIN 1609 1767 RNase III 2. {ECO:0000255|PROSITE-
ProRule:PRU00177}.
DOMAIN 1792 1857 DRBM. {ECO:0000255|PROSITE-
ProRule:PRU00266}.
NP_BIND 54 61 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 161 164 DECH box.
COMPBIAS 1394 1402 Poly-Asp.
METAL 1298 1298 Magnesium or manganese 1. {ECO:0000250}.
METAL 1377 1377 Magnesium or manganese 1. {ECO:0000250}.
METAL 1380 1380 Magnesium or manganese 1. {ECO:0000250}.
METAL 1648 1648 Magnesium or manganese 2. {ECO:0000250}.
METAL 1753 1753 Magnesium or manganese 2. {ECO:0000250}.
METAL 1756 1756 Magnesium or manganese 2. {ECO:0000250}.
SITE 1749 1749 Important for activity. {ECO:0000250}.
CONFLICT 739 751 IPECLRGCYPVPE -> VK (in Ref. 2;
AAQ90464). {ECO:0000305}.
CONFLICT 921 921 R -> K (in Ref. 2; AAQ90464).
{ECO:0000305}.
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


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