DICER_XENTR
ID DICER_XENTR Reviewed; 1893 AA.
AC B3DLA6; C0IN01;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 2.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=Endoribonuclease Dicer;
DE EC=3.1.26.3;
GN Name=dicer1;
OS Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX NCBI_TaxID=8364;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA Garcia M.A., Kidwell M.A., Heintzman S.E., Wormington M.;
RT "Activation of miRNA processing during Xenopus oocyte maturation.";
RL Submitted (DEC-2007) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=N6; TISSUE=Intestine;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases.
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=B3DLA6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=B3DLA6-2; Sequence=VSP_037298, VSP_037299;
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00657}.
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DR EMBL; EU338242; ACA52289.1; -; mRNA.
DR EMBL; BC167373; AAI67373.1; -; mRNA.
DR RefSeq; NP_001123390.2; NM_001129918.2. [B3DLA6-1]
DR AlphaFoldDB; B3DLA6; -.
DR SMR; B3DLA6; -.
DR STRING; 8364.ENSXETP00000050382; -.
DR PaxDb; B3DLA6; -.
DR PRIDE; B3DLA6; -.
DR Ensembl; ENSXETT00000096069; ENSXETP00000082776; ENSXETG00000023315.
DR GeneID; 100170154; -.
DR KEGG; xtr:100170154; -.
DR CTD; 23405; -.
DR Xenbase; XB-GENE-491114; dicer1.
DR eggNOG; KOG0701; Eukaryota.
DR InParanoid; B3DLA6; -.
DR OrthoDB; 1337630at2759; -.
DR Reactome; R-XTR-203927; MicroRNA (miRNA) biogenesis.
DR Reactome; R-XTR-426486; Small interfering RNA (siRNA) biogenesis.
DR Proteomes; UP000008143; Chromosome 8.
DR Proteomes; UP000790000; Unplaced.
DR Bgee; ENSXETG00000023315; Expressed in egg cell and 14 other tissues.
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: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:0098795; P:global gene silencing by mRNA cleavage; ISS:UniProtKB.
DR GO; GO:0031054; P:pre-miRNA processing; ISS:UniProtKB.
DR GO; GO:0090501; P:RNA phosphodiester bond hydrolysis; IBA:GO_Central.
DR GO; GO:0030422; P:siRNA processing; ISS:UniProtKB.
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 Alternative splicing; ATP-binding; Cytoplasm; Endonuclease; Helicase;
KW Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease;
KW Nucleotide-binding; Phosphoprotein; Reference proteome; Repeat;
KW RNA-binding; RNA-mediated gene silencing.
FT CHAIN 1..1893
FT /note="Endoribonuclease Dicer"
FT /id="PRO_0000373986"
FT DOMAIN 41..217
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 424..593
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 621..713
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 892..1036
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 1249..1380
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1637..1795
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1820..1885
FT /note="DRBM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 400..424
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 718..737
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 165..168
FT /note="DECH box"
FT COMPBIAS 402..418
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 1293
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1371
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1374
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1676
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 1781
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 1784
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT SITE 1777
FT /note="Important for activity"
FT /evidence="ECO:0000250"
FT VAR_SEQ 804..811
FT /note="IPHFPVYT -> VLQCTIKF (in isoform 2)"
FT /evidence="ECO:0000303|Ref.2"
FT /id="VSP_037298"
FT VAR_SEQ 812..1893
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.2"
FT /id="VSP_037299"
SQ SEQUENCE 1893 AA; 215398 MW; EAA01EFBC49FF8F3 CRC64;
MAGLQLMTPA SSPMGPFFGL PWQQEAIHDN IYTPRKYQVE LLEAALDHNT IVCLNSGSGK
TFIAVLLSKE LSYQIRGDFS KNTKRTVFLV NSEKQVSQQV SAVRTHTDLK VGEYSDQEKT
QCWAKERWYL EFETHQVLVM TCHIFLNVLK SGNVSLSNIN LLVFDECHLA IQDHPYREIM
KICESCQPCP RILGLTASIL NGKCDPRDLE EKIQKLEEIL RSNAETATDL VVLDRYASQP
CEIVLDCGPY IDKSGLYQRL LNELDEALNF LIDCNISTHS KERDSTLISK QILSDCQTVL
LVLGPWCADK VAGMMVRELQ KYIKHEQEEL HRKFLLFTDT ILRKIHALCE EHFSPASLDM
KFVTPKVIKL LEILRKYKPY ERQQFESVEW YNNRNQDNYV SWSDSEDDDD EDEEIEEKEK
TETSFPSPFT NILCGIIFVE RRYTAVVLNR LIKEAGKQDP ELAYISSNFI TGHGIGKNQP
RNKQMEVEFR KQEEVLRKFR AHETNLLIAT SIVEEGVDIP KCNLVVRFDL PSEYRSYVQS
KGRARAPISN YIMLADSDKI KAFEEDLKTY KAIEKILRNK CSKSIDCGNT ESEPIVDDDE
IFPPYVLRQD DGSPRVTINT AIGHINRYCA RLPSDPFTHL APKCKTREFP DGLYRSTLYL
PINSPLRAPI VGPPMNCGRL ADRAVALICC KKLHEIGELD DHLMPVGKET VKYEEELDLH
DEEETSVPGR PGSTKRRQCY PKAIPECLRN SYPKPGQPCY LYVIGMVLTT PLPDELNFRR
RKLYPPEDTT RCFGILTAKP IPQIPHFPVY TRSGEVTISI ELKKSGFTLN LEQLELITRL
HQYIFSHILR LEKPALEFKP TVADCAYCVL PLNVVNDSGT LDIDFKFVED IEKSEARTGI
PNTQYSAESP FIFKLEDYQD AVIIPRQVIY RNFDQPHRFY VADVYTDLTP LSKFPSPEYE
TFAEYYKTKY NLDLTNLNQP LLDVDHTSSR LNLLTPRHLN QKGKALPLSS AEKRKAKWES
LQNKQILVPE LCAIHPVPAS LWRKAVCLPS ILYRLHCLLT AEELRAQTAI DAGVGVKSLP
DDFRYPNLDF GWKRSIDSKT FISNQSSSSV ESESDCRLNK TTAPDSAASS AANSVIYMQI
NDQMSVNCTP PCQKSLSHLQ TVCFSDDYKA INGISCNGLT NGDWEAESAA CFQKDERITC
KQEIPEKSTS FHVQNLPKEN QPILKECTLS NSDGNVSKPT SDECPSTCTS DMHYDSGLSN
RHSSKTLGPN PGLILQALTL SNASDGFNLE RLEMLGDSFL KHAITTYLFC TYPDAHEGRL
SYMRSKKVSN CNLYRLGKKK GSPSRMVVSI FDPPVNWLPP GYIVNQDKNS DKWESNETSG
EDVMVNGKID EDFDDEEDED LMWRNPKEET DFDDDFLEYD QEHIKFIDSM LMGSGAFVKK
IPLSSFAPPD QNYEWRAPKK PPLESSQFPC DFDDFDYSSW DAMCYLDPSK AVEEDDFVVG
FWNPSEENCG ADAGKQSISY DLHTEQCIAD KSIADCVEAL LGCYLTSCGE RAAQLFLCSL
GLKVLPEVRK LVTNTNVISA SSSYQNSTRD NCTLTARTNT DLSSCKGIDY GYLKIPPRCM
FEHPDAEKTL DHLISGFENF EKKINYPFKN KAYLLQAFTH ASYHYNTITD CYQRLEFLGD
AILDYLITKH LYEDPRQHSP GVLTDLRSAL VNNTIFASLA VKYDYHKYFK AISPELFHVI
DDFVQFQLEK NEMQGMDSEL RRSEEDEEKE EDIEVPKAMG DIFESLAGAI YMDSGMSLET
VWHVYYPMMQ PLIEKFSANV PRSPVRELLE MEPETAKFSP AERTYDGKVR VTVEVVGKGK
FKGVGRSYRI AKSAAARRAL RSLKANQSQV PNS
