DCR1_CAEEL
ID DCR1_CAEEL Reviewed; 1910 AA.
AC P34529;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2012, sequence version 3.
DT 03-AUG-2022, entry version 183.
DE RecName: Full=Endoribonuclease dcr-1;
DE EC=3.1.26.- {ECO:0000269|PubMed:11641272, ECO:0000269|PubMed:20223951};
DE Contains:
DE RecName: Full=Death-promoting deoxyribonuclease {ECO:0000305|PubMed:20223951};
DE Short=tDCR-1 {ECO:0000303|PubMed:20223951};
DE EC=3.1.21.- {ECO:0000269|PubMed:20223951};
GN Name=dcr-1 {ECO:0000303|PubMed:11641272, ECO:0000312|WormBase:K12H4.8};
GN Synonyms=eri-4 {ECO:0000312|WormBase:K12H4.8},
GN let-740 {ECO:0000312|WormBase:K12H4.8};
GN ORFNames=K12H4.8 {ECO:0000312|WormBase:K12H4.8};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=7906398; DOI=10.1038/368032a0;
RA Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J.,
RA Burton J., Connell M., Copsey T., Cooper J., Coulson A., Craxton M.,
RA Dear S., Du Z., Durbin R., Favello A., Fraser A., Fulton L., Gardner A.,
RA Green P., Hawkins T., Hillier L., Jier M., Johnston L., Jones M.,
RA Kershaw J., Kirsten J., Laisster N., Latreille P., Lightning J., Lloyd C.,
RA Mortimore B., O'Callaghan M., Parsons J., Percy C., Rifken L., Roopra A.,
RA Saunders D., Shownkeen R., Sims M., Smaldon N., Smith A., Smith M.,
RA Sonnhammer E., Staden R., Sulston J., Thierry-Mieg J., Thomas K.,
RA Vaudin M., Vaughan K., Waterston R., Watson A., Weinstock L.,
RA Wilkinson-Sproat J., Wohldman P.;
RT "2.2 Mb of contiguous nucleotide sequence from chromosome III of C.
RT elegans.";
RL Nature 368:32-38(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [3]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=11641272; DOI=10.1101/gad.927801;
RA Ketting R.F., Fischer S.E.J., Bernstein E., Sijen T., Hannon G.J.,
RA Plasterk R.H.A.;
RT "Dicer functions in RNA interference and in synthesis of small RNA involved
RT in developmental timing in C. elegans.";
RL Genes Dev. 15:2654-2659(2001).
RN [4]
RP FUNCTION, AND INTERACTION WITH PIR-1.
RX PubMed=16439208; DOI=10.1016/j.cell.2005.11.036;
RA Duchaine T.F., Wohlschlegel J.A., Kennedy S., Bei Y., Conte D. Jr.,
RA Pang K., Brownell D.R., Harding S., Mitani S., Ruvkun G., Yates J.R. III,
RA Mello C.C.;
RT "Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in
RT multiple small-RNA-mediated pathways.";
RL Cell 124:343-354(2006).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, PROTEOLYTIC CLEAVAGE, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF ASP-1537; GLU-1682; ASP-1686 AND GLU-1794.
RX PubMed=20223951; DOI=10.1126/science.1182374;
RA Nakagawa A., Shi Y., Kage-Nakadai E., Mitani S., Xue D.;
RT "Caspase-dependent conversion of Dicer ribonuclease into a death-promoting
RT deoxyribonuclease.";
RL Science 328:327-334(2010).
RN [6]
RP FUNCTION.
RX PubMed=23918784; DOI=10.1128/iai.00700-13;
RA Iatsenko I., Sinha A., Roedelsperger C., Sommer R.J.;
RT "New role for DCR-1/dicer in Caenorhabditis elegans innate immunity against
RT the highly virulent bacterium Bacillus thuringiensis DB27.";
RL Infect. Immun. 81:3942-3957(2013).
RN [7]
RP FUNCTION, IDENTIFICATION IN THE ERI/DICER COMPLEX, AND INTERACTION WITH
RP PIR-1.
RX PubMed=33378643; DOI=10.1016/j.molcel.2020.12.004;
RA Chaves D.A., Dai H., Li L., Moresco J.J., Oh M.E., Conte D. Jr.,
RA Yates J.R. III, Mello C.C., Gu W.;
RT "The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C.
RT elegans.";
RL Mol. Cell 0:0-0(2020).
RN [8]
RP FUNCTION, AND MUTAGENESIS OF GLY-492.
RX PubMed=32908307; DOI=10.1038/s41586-020-2699-5;
RA Kaletsky R., Moore R.S., Vrla G.D., Parsons L.R., Gitai Z., Murphy C.T.;
RT "C. elegans interprets bacterial non-coding RNAs to learn pathogenic
RT avoidance.";
RL Nature 586:445-451(2020).
CC -!- FUNCTION: Component of the ERI/DICER complex which is involved in
CC processing amplified double-stranded RNA (dsRNA) intermediates during
CC small-RNA-mediated gene-silencing or RNA interference (RNAi)
CC (Probable). Involved in cleaving dsRNA in the RNAi pathway
CC (PubMed:11641272, PubMed:20223951). It produces 21 to 23 bp dsRNAs
CC (siRNAs) which target the selective destruction of homologous RNAs
CC (PubMed:11641272, PubMed:20223951). Seems to process the precursor of
CC the small temporal RNA let-7 which is involved in developmental timing
CC (PubMed:11641272). Required for avoidance behavior induced by small
CC RNAs derived from pathogenic bacteria such as P.aeruginosa
CC (PubMed:32908307). Involved in innate immunity through its role in
CC small RNA processing. {ECO:0000269|PubMed:11641272,
CC ECO:0000269|PubMed:20223951, ECO:0000269|PubMed:23918784,
CC ECO:0000269|PubMed:32908307, ECO:0000305|PubMed:16439208,
CC ECO:0000305|PubMed:33378643}.
CC -!- FUNCTION: tDCR-1 acts as a deoxyribonuclease (DNase) initiating DNA
CC fragmentation during apoptosis, upstream of nucleases cps-6, crn-2 and
CC nuc-1. {ECO:0000269|PubMed:20223951}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:20223951};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q9UPY3};
CC -!- SUBUNIT: Component of the ERI/DICER complex at least composed of dcr-1,
CC rrf-3 and eri-1 (Probable). Interacts with pir-1 (PubMed:16439208,
CC PubMed:33378643). {ECO:0000269|PubMed:16439208,
CC ECO:0000269|PubMed:33378643, ECO:0000305|PubMed:33378643}.
CC -!- INTERACTION:
CC P34529; G5EDI8: drh-1; NbExp=9; IntAct=EBI-326716, EBI-327837;
CC P34529; O44406: eri-1; NbExp=4; IntAct=EBI-326716, EBI-863689;
CC P34529; Q9GZI7: eri-3; NbExp=5; IntAct=EBI-326716, EBI-866569;
CC P34529; Q95XS0: eri-5; NbExp=8; IntAct=EBI-326716, EBI-866573;
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown in a cps-6 mutant
CC background reduces the number of DNA breaks in embryonic cells
CC undergoing apoptosis. {ECO:0000269|PubMed:20223951}.
CC -!- MISCELLANEOUS: The avoidance behavior is transgenerationally inherited,
CC and thus progeny display this same aversion despite never been exposed
CC to this pathogenic bacteria. {ECO:0000269|PubMed:32908307}.
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000305}.
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DR EMBL; BX284603; CCD71200.2; -; Genomic_DNA.
DR PIR; S44849; S44849.
DR RefSeq; NP_498761.2; NM_066360.3.
DR AlphaFoldDB; P34529; -.
DR BioGRID; 41344; 131.
DR DIP; DIP-25340N; -.
DR IntAct; P34529; 86.
DR STRING; 6239.K12H4.8; -.
DR EPD; P34529; -.
DR PaxDb; P34529; -.
DR PeptideAtlas; P34529; -.
DR EnsemblMetazoa; K12H4.8.1; K12H4.8.1; WBGene00000939.
DR GeneID; 176138; -.
DR KEGG; cel:CELE_K12H4.8; -.
DR UCSC; K12H4.8; c. elegans.
DR CTD; 42693; -.
DR WormBase; K12H4.8; CE47418; WBGene00000939; dcr-1.
DR eggNOG; KOG0701; Eukaryota.
DR GeneTree; ENSGT00940000156287; -.
DR HOGENOM; CLU_000907_4_4_1; -.
DR InParanoid; P34529; -.
DR OMA; TTYLYCT; -.
DR OrthoDB; 1337630at2759; -.
DR PhylomeDB; P34529; -.
DR Reactome; R-CEL-203927; MicroRNA (miRNA) biogenesis.
DR Reactome; R-CEL-426486; Small interfering RNA (siRNA) biogenesis.
DR SignaLink; P34529; -.
DR PRO; PR:P34529; -.
DR Proteomes; UP000001940; Chromosome III.
DR Bgee; WBGene00000939; Expressed in germ line (C elegans) and 4 other tissues.
DR GO; GO:0005737; C:cytoplasm; IDA:WormBase.
DR GO; GO:0005829; C:cytosol; IDA:WormBase.
DR GO; GO:0005634; C:nucleus; IDA:WormBase.
DR GO; GO:0016442; C:RISC complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004530; F:deoxyribonuclease I activity; IDA:WormBase.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
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; IDA:WormBase.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0006309; P:apoptotic DNA fragmentation; IGI:WormBase.
DR GO; GO:0050830; P:defense response to Gram-positive bacterium; IMP:UniProtKB.
DR GO; GO:0000737; P:DNA catabolic process, endonucleolytic; IDA:WormBase.
DR GO; GO:0035262; P:gonad morphogenesis; IMP:WormBase.
DR GO; GO:0034470; P:ncRNA processing; IDA:WormBase.
DR GO; GO:0002119; P:nematode larval development; IMP:WormBase.
DR GO; GO:0008355; P:olfactory learning; IMP:WormBase.
DR GO; GO:2000636; P:positive regulation of primary miRNA processing; IMP:WormBase.
DR GO; GO:0031054; P:pre-miRNA processing; IMP:WormBase.
DR GO; GO:0040034; P:regulation of development, heterochronic; IMP:WormBase.
DR GO; GO:0000003; P:reproduction; IMP:WormBase.
DR GO; GO:0006401; P:RNA catabolic process; IDA:WormBase.
DR GO; GO:0090501; P:RNA phosphodiester bond hydrolysis; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IEA:InterPro.
DR GO; GO:0030422; P:siRNA processing; IMP:WormBase.
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 HAMAP; MF_00104; RNase_III; 1.
DR InterPro; IPR038248; Dicer_dimer_sf.
DR InterPro; IPR005034; Dicer_dimerisation_dom.
DR InterPro; IPR044441; DICER_DSRM.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR006935; Helicase/UvrB_N.
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; IPR011907; RNase_III.
DR InterPro; IPR000999; RNase_III_dom.
DR InterPro; IPR036389; RNase_III_sf.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF02170; PAZ; 1.
DR Pfam; PF04851; ResIII; 1.
DR Pfam; PF00636; Ribonuclease_3; 2.
DR SMART; SM00487; DEXDc; 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 1: Evidence at protein level;
KW Apoptosis; ATP-binding; Coiled coil; Endonuclease; Helicase; Hydrolase;
KW Magnesium; Manganese; Metal-binding; Nuclease; Nucleotide-binding;
KW Reference proteome; Repeat; RNA-binding; RNA-mediated gene silencing.
FT CHAIN 1..1910
FT /note="Endoribonuclease dcr-1"
FT /id="PRO_0000180473"
FT CHAIN 1538..1910
FT /note="Death-promoting deoxyribonuclease"
FT /evidence="ECO:0000305"
FT /id="PRO_0000441121"
FT DOMAIN 20..201
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 371..542
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 571..667
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 847..1003
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 1381..1589
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1643..1805
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1833..1896
FT /note="DRBM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 951..988
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1227..1248
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1272..1310
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 1245..1280
FT /evidence="ECO:0000255"
FT MOTIF 145..148
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 1227..1247
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1272..1290
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 33..40
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1682
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:20223951"
FT BINDING 1791
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9UPY3"
FT BINDING 1794
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:20223951"
FT SITE 1537..1538
FT /note="Cleavage; by ced-3"
FT /evidence="ECO:0000269|PubMed:20223951"
FT SITE 1787
FT /note="Important for activity"
FT /evidence="ECO:0000250|UniProtKB:Q8R418"
FT MUTAGEN 492
FT /note="G->R: In mg375; defective avoidance behavior in
FT response to P.aeruginosa."
FT /evidence="ECO:0000269|PubMed:32908307"
FT MUTAGEN 1537
FT /note="D->E: Loss of cleavage by ced-3. Loss of
FT deoxyribonuclease (DNase) activity. Reduced number of cell
FT corpses in embryos."
FT /evidence="ECO:0000269|PubMed:20223951"
FT MUTAGEN 1682
FT /note="E->A: Severe reduction in both dsRNA dicing and
FT DNase activities; when associated with A-1794. Loss of
FT dsRNA dicing and DNase activities, bursting and protruding
FT vulva and reduction in the number of cell corpses in
FT embryos; when associated with A-1794 and A-1686."
FT /evidence="ECO:0000269|PubMed:20223951"
FT MUTAGEN 1686
FT /note="D->A: Loss of dsRNA dicing and DNase activities,
FT bursting and protruding vulva and reduction in the number
FT of cell corpses in embryos; when associated with A-1794 and
FT A-1682."
FT /evidence="ECO:0000269|PubMed:20223951"
FT MUTAGEN 1794
FT /note="E->A: Severe reduction in both dsRNA dicing and
FT DNase activities; when associated with A-1682. Loss of
FT dsRNA dicing and DNase activities, bursting and protruding
FT vulva and reduction in the number of cell corpses in
FT embryos; when associated with A-1682 and A-1686."
FT /evidence="ECO:0000269|PubMed:20223951"
SQ SEQUENCE 1910 AA; 218423 MW; B49D19D7B3730F80 CRC64;
MVRVRADLQC FNPRDYQVEL LDKATKKNTI VQLGTGSGKT FIAVLLLKEY GVQLFAPLDQ
GGKRAFFVVE KVNLVEQQAI HIEVHTSFKV GQVHGQTSSG LWDSKEQCDQ FMKRHHVVVI
TAQCLLDLIR HAYLKIEDMC VLIFDECHHA LGSQHPYRSI MVDYKLLKKD KPVPRVLGLT
ASLIKAKVAP EKLMEQLKKL ESAMDSVIET ASDLVSLSKY GAKPYEVVII CKDFEIGCLG
IPNFDTVIEI FDETVAFVNT TTEFHPDLDL DPRRPIKDSL KTTRAVFRQL GPWAAWRTAQ
VWEKELGKII KSQVLPDKTL RFLNMAKTSM ITIKRLLEPE MKKIKSIEAL RPYVPQRVIR
LFEILETFNP EFQKERMKLE KAEHLSAIIF VDQRYIAYSL LLMMRHIKSW EPKFKFVNPD
YVVGASGRNL ASSDSQGLHK RQTEVLRRFH RNEINCLIAT SVLEEGVDVK QCNLVIKFDR
PLDMRSYVQS KGRARRAGSR YVITVEEKDT AACDSDLKDF QQIEKILLSR HRTVNNPIED
DSDRFEEFDV DSQMEPYVVE KTGATLKMST AIALINRYCS KLPSDIFTRL VPHNQIIPIE
ENGVTKYCAE LLLPINSPIK HAIVLKNPMP NKKTAQMAVA LEACRQLHLE GELDDNLLPK
GRESIAKLLE HIDEEPDEYA PGIAAKVGSS KRKQLYDKKI ARALNESFVE ADKECFIYAF
ELERFREAEL TLNPKRRKFE DPFNYEYCFG FLSAKEIPKI PPFPVFLRQG NMKVRLIVAP
KKTTVTAAQL QEIQLFHNYL FTQVLQMCKT GNLEFDGTSN APLNTLIVPL NKRKDDMSYT
INMKYVSEVV ANMENMPRIP KDEVRRQYKF NAEDYKDAIV MPWYRNLEQP VFYYVAEILP
EWRPSSKFPD THFETFNEYF IKKYKLEIYD QNQSLLDVDF TSTRLNLLQP RIQNQPRRSR
TVSNSSTSNI PQASASDSKE SNTSVPHSSQ RQILVPELMD IHPISATLWN VIAALPSIFY
RVNQLLLTDE LRETILVKAF GKEKTKLDDN VEWNSLAYAT EYEEKQTIIV KKIQQLRDLN
QKSIEDQERE TRENDKIDDG EELFNIGVWD PEEAVRIGVE ISSRDDRMDG EDQDTVGLTQ
GLHDGNISDE DDELPFVMHD YTARLTSNRN GIGAWSGSES IVPSGWGDWD GPEPDNSPMP
FQILGGPGGL NVQALMADVG RVFDPSTASS SLSQTVQEST VSPPKQLTKE EEQFKKLQND
LLKQAKERLE ALEMSEDMEK PRRLEDTVNL EDYGDDQENQ EDENTPTNFP KTIDEEIEEL
SIGARKKQEI DDNAAKTDVL ERENCEVLPV AINEKSRSFS FEKESKAING RLIRQRSEEY
VSHIDSDIGL GVSPCLLLTA LTTSNAADGM SLERFETIGD SFLKFATTDY LYHTLLDQHE
GKLSFARSKE VSNCNLYRLG KKLGIPQLIV ANKFDAHDSW LPPCYIPTCD FKAPNTDDAE
EKDNEIERIL DGQVIEEKPE NKTGWDIGGD VSKSTTDGIE TITFPKQARV GNDDISPLPY
NLLTQQHISD KSIADAVEAL IGVHLLTLGP NPTLKVMNWM GLKVIQKDQK SDVPSPLLRF
IDTPTNPNAS LNFLNNLWQQ FQFTQLEEKI GYRFKERAYL VQAFTHASYI NNRVTGCYQR
LEFLGDAVLD YMITRYLFED SRQYSPGVLT DLRSALVNNT IFASLAVKFE FQKHFIAMCP
GLYHMIEKFV KLCSERNFDT NFNAEMYMVT TEEEIDEGQE EDIEVPKAMG DIFESVAGAI
YLDSGRNLDT TWQVIFHMMR GTIELCCANP PRSPIRELME FEQSKVRFSK MERILESGKV
RVTVEVVNNM RFTGMGRNYR IAKATAAKRA LKYLHQIEQQ RRQSPSLTTV
