DCL3_ARATH
ID DCL3_ARATH Reviewed; 1580 AA.
AC Q9LXW7;
DT 08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT 08-FEB-2011, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Endoribonuclease Dicer homolog 3;
DE EC=3.1.26.-;
DE AltName: Full=Dicer-like protein 3;
DE Short=AtDCL3;
GN Name=DCL3; OrderedLocusNames=At3g43920; ORFNames=T15B3.60;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
RX PubMed=16638569; DOI=10.1016/j.febslet.2006.03.072;
RA Margis R., Fusaro A.F., Smith N.A., Curtin S.J., Watson J.M.,
RA Finnegan E.J., Waterhouse P.M.;
RT "The evolution and diversification of Dicers in plants.";
RL FEBS Lett. 580:2442-2450(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP SUBCELLULAR LOCATION.
RX PubMed=15024409; DOI=10.1371/journal.pbio.0020104;
RA Xie Z., Johansen L.K., Gustafson A.M., Kasschau K.D., Lellis A.D.,
RA Zilberman D., Jacobsen S.E., Carrington J.C.;
RT "Genetic and functional diversification of small RNA pathways in plants.";
RL PLoS Biol. 2:E104-E104(2004).
RN [5]
RP FUNCTION.
RX PubMed=16040244; DOI=10.1016/j.cub.2005.07.024;
RA Gasciolli V., Mallory A.C., Bartel D.P., Vaucheret H.;
RT "Partially redundant functions of Arabidopsis DICER-like enzymes and a role
RT for DCL4 in producing trans-acting siRNAs.";
RL Curr. Biol. 15:1494-1500(2005).
RN [6]
RP INTERACTION WITH DRB2 AND DRB5.
RX PubMed=15821876; DOI=10.1007/s11103-004-6853-5;
RA Hiraguri A., Itoh R., Kondo N., Nomura Y., Aizawa D., Murai Y., Koiwa H.,
RA Seki M., Shinozaki K., Fukuhara T.;
RT "Specific interactions between Dicer-like proteins and HYL1/DRB-family
RT dsRNA-binding proteins in Arabidopsis thaliana.";
RL Plant Mol. Biol. 57:173-188(2005).
RN [7]
RP SUBCELLULAR LOCATION.
RX PubMed=16839878; DOI=10.1016/j.cell.2006.05.031;
RA Pontes O., Li C.F., Nunes P.C., Haag J., Ream T., Vitins A., Jacobsen S.E.,
RA Pikaard C.S.;
RT "The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a
RT nucleolar RNA processing center.";
RL Cell 126:79-92(2006).
RN [8]
RP FUNCTION.
RX PubMed=16810317; DOI=10.1038/sj.emboj.7601217;
RA Bouche N., Lauressergues D., Gasciolli V., Vaucheret H.;
RT "An antagonistic function for Arabidopsis DCL2 in development and a new
RT function for DCL4 in generating viral siRNAs.";
RL EMBO J. 25:3347-3356(2006).
RN [9]
RP FUNCTION.
RX PubMed=17579240; DOI=10.1534/genetics.107.070649;
RA Schmitz R.J., Hong L., Fitzpatrick K.E., Amasino R.M.;
RT "DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via
RT repression of FLOWERING LOCUS C in Arabidopsis thaliana.";
RL Genetics 176:1359-1362(2007).
RN [10]
RP FUNCTION.
RX PubMed=17586651; DOI=10.1105/tpc.106.047449;
RA Diaz-Pendon J.A., Li F., Li W.X., Ding S.W.;
RT "Suppression of antiviral silencing by cucumber mosaic virus 2b protein in
RT Arabidopsis is associated with drastically reduced accumulation of three
RT classes of viral small interfering RNAs.";
RL Plant Cell 19:2053-2063(2007).
RN [11]
RP FUNCTION.
RX PubMed=18353962; DOI=10.1128/jvi.00272-08;
RA Donaire L., Barajas D., Martinez-Garcia B., Martinez-Priego L., Pagan I.,
RA Llave C.;
RT "Structural and genetic requirements for the biogenesis of tobacco rattle
RT virus-derived small interfering RNAs.";
RL J. Virol. 82:5167-5177(2008).
RN [12]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
CC -!- FUNCTION: Ribonuclease (RNase) III involved in RNA-mediated post-
CC transcriptional gene silencing (PTGS). Involved in the processing of
CC repeat-associated small interfering RNAs (ra-siRNAs, derived from
CC heterochromatin and DNA repeats such as transposons) by cleaving small
CC dsRNAs into 24 nucleotide ra-siRNAs. Plays a role in antiviral RNA
CC silencing. Involved in the production of viral siRNAs derived from the
CC cabbage leaf curl virus (CaLCuV) and tobacco rattle virus (TRV).
CC Targeted by the viral silencing suppressor (VSR) protein 2b of the
CC cucumber mosaic virus (CMV) that inactivates DCL3 function in RNA
CC silencing. Acts redundantly with DICER-LIKE 1 (DCL1) to promote
CC flowering via repression of FLOWERING LOCUS C (FLC). Does not seem to
CC be involved in microRNAs (miRNAs) processing.
CC {ECO:0000269|PubMed:16040244, ECO:0000269|PubMed:16810317,
CC ECO:0000269|PubMed:17579240, ECO:0000269|PubMed:17586651,
CC ECO:0000269|PubMed:18353962}.
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 -!- SUBUNIT: Interacts with DRB2 and DRB5. {ECO:0000269|PubMed:15821876}.
CC -!- INTERACTION:
CC Q9LXW7; Q9LJF5: DRB3; NbExp=2; IntAct=EBI-632737, EBI-10815073;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:15024409,
CC ECO:0000269|PubMed:16839878}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LXW7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LXW7-2; Sequence=VSP_040616, VSP_040617;
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000305}.
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DR EMBL; DQ479972; ABF19799.1; -; mRNA.
DR EMBL; AL163975; CAB88120.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE77842.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE77843.1; -; Genomic_DNA.
DR PIR; T48946; T48946.
DR RefSeq; NP_001154662.2; NM_001161190.2. [Q9LXW7-1]
DR RefSeq; NP_189978.1; NM_114260.1. [Q9LXW7-2]
DR AlphaFoldDB; Q9LXW7; -.
DR SMR; Q9LXW7; -.
DR BioGRID; 8828; 5.
DR IntAct; Q9LXW7; 3.
DR MINT; Q9LXW7; -.
DR STRING; 3702.AT3G43920.2; -.
DR PaxDb; Q9LXW7; -.
DR ProteomicsDB; 223983; -. [Q9LXW7-1]
DR EnsemblPlants; AT3G43920.1; AT3G43920.1; AT3G43920. [Q9LXW7-2]
DR EnsemblPlants; AT3G43920.2; AT3G43920.2; AT3G43920. [Q9LXW7-1]
DR GeneID; 823508; -.
DR Gramene; AT3G43920.1; AT3G43920.1; AT3G43920. [Q9LXW7-2]
DR Gramene; AT3G43920.2; AT3G43920.2; AT3G43920. [Q9LXW7-1]
DR KEGG; ath:AT3G43920; -.
DR Araport; AT3G43920; -.
DR TAIR; locus:2097139; AT3G43920.
DR eggNOG; KOG0701; Eukaryota.
DR InParanoid; Q9LXW7; -.
DR OMA; TRKNHAY; -.
DR OrthoDB; 1337630at2759; -.
DR PhylomeDB; Q9LXW7; -.
DR PRO; PR:Q9LXW7; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LXW7; baseline and differential.
DR Genevisible; Q9LXW7; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003725; F:double-stranded RNA binding; IDA:TAIR.
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:0051607; P:defense response to virus; IMP:TAIR.
DR GO; GO:0010216; P:maintenance of DNA methylation; IMP:TAIR.
DR GO; GO:0051214; P:RNAi-mediated antiviral immunity against RNA virus; IGI:TAIR.
DR GO; GO:0030422; P:siRNA processing; IMP:TAIR.
DR GO; GO:0010267; P:ta-siRNA processing; IMP:TAIR.
DR CDD; cd00593; RIBOc; 2.
DR Gene3D; 1.10.1520.10; -; 2.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_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; 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; 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 Alternative splicing; ATP-binding; Endonuclease; Helicase; Hydrolase;
KW Magnesium; Manganese; Metal-binding; Nuclease; Nucleotide-binding; Nucleus;
KW Plant defense; Reference proteome; Repeat; RNA-binding;
KW RNA-mediated gene silencing.
FT CHAIN 1..1580
FT /note="Endoribonuclease Dicer homolog 3"
FT /id="PRO_0000404661"
FT DOMAIN 51..223
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 394..562
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 821..934
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 985..1157
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1198..1340
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 581..601
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 613..638
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 170..173
FT /note="DECH box"
FT COMPBIAS 581..595
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 613..630
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 64..71
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1234
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1326
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1329
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1322
FT /note="Important for activity"
FT /evidence="ECO:0000250"
FT VAR_SEQ 101..103
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16638569"
FT /id="VSP_040616"
FT VAR_SEQ 186..231
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16638569"
FT /id="VSP_040617"
SQ SEQUENCE 1580 AA; 177425 MW; EA71D47BF3C29FA5 CRC64;
MHSSLEPEKM EEGGGSNSLK RKFSEIDGDQ NLDSVSSPMM TDSNGSYELK VYEVAKNRNI
IAVLGTGIDK SEITKRLIKA MGSSDTDKRL IIFLAPTVNL VKQQCCEIRA LVNLKVEEYF
GAKGVDKWTS QRWDEEFSKH DVLVMTPQIL LDVLRSAFLK LEMVCLLIID ECHHTTGNHP
YAKLMKEFYH ESTSKPKIFG LTASAVIRKG IVSSPSNYAA QVSELERLMD SKIFNPEERE
GVEKFATTVK EGPILYNPSP SCSLELKEKL ETSHLKFDAS LRRLQELGKD SFLNMDNKFE
TYQKRLSIDY REILHCLDNL GLICAHLAAE VCLEKISDTK EESETYKECS MVCKEFLEDI
LSTIGVYLPQ DDKSLVDLQQ NHLSAVISGH VSPKLKELFH LLDSFRGDKQ KQCLILVERI
ITAKVIERFV KKEASLAYLN VLYLTENNPS TNVSAQKMQI EIPDLFQHGK VNLLFITDVV
EEGFQVPDCS CMVCFDLPKT MCSYSQSQKH AKQSNSKSIM FLERGNPKQR DHLHDLMRRE
VLIQDPEAPN LKSCPPPVKN GHGVKEIGSM VIPDSNITVS EEAASTQTMS DPPSRNEQLP
PCKKLRLDNN LLQSNGKEKV ASSKSKSSSS AAGSKKRKEL HGTTCANALS GTWGENIDGA
TFQAYKFDFC CNISGEVYSS FSLLLESTLA EDVGKVEMDL YLVRKLVKAS VSPCGQIRLS
QEELVKAKYF QQFFFNGMFG KLFVGSKSQG TKREFLLQTD TSSLWHPAFM FLLLPVETND
LASSATIDWS AINSCASIVE FLKKNSLLDL RDSDGNQCNT SSGQEVLLDD KMEETNLIHF
ANASSDKNSL EELVVIAIHT GRIYSIVEAV SDSSAMSPFE VDASSGYATY AEYFNKKYGI
VLAHPNQPLM KLKQSHHAHN LLVDFNEEMV VKTEPKAGNV RKRKPNIHAH LPPELLARID
VPRAVLKSIY LLPSVMHRLE SLMLASQLRE EIDCSIDNFS ISSTSILEAV TTLTCPESFS
MERLELLGDS VLKYVASCHL FLKYPDKDEG QLSRQRQSII SNSNLHRLTT SRKLQGYIRN
GAFEPRRWTA PGQFSLFPVP CKCGIDTREV PLDPKFFTEN MTIKIGKSCD MGHRWVVSKS
VSDCAEALIG AYYVSGGLSA SLHMMKWLGI DVDFDPNLVV EAINRVSLRC YIPKEDELIE
LERKIQHEFS AKFLLKEAIT HSSLRESYSY ERLEFLGDSV LDFLITRHLF NTYEQTGPGE
MTDLRSACVN NENFAQVAVK NNLHTHLQRC ATVLETQIND YLMSFQKPDE TGRSIPSIQG
PKALGDVVES IAGALLIDTR LDLDQVWRVF EPLLSPLVTP DKLQLPPYRE LNELCDSLGY
FFRVKCSNDG VKAQATIQLQ LDDVLLTGDG SEQTNKLALG KAASHLLTQL EKRNISRKTS
LGDNQSSMDV NLACNHSDRE TLTSETTEIQ SIVIPFIGPI NMKKGGPRGT LHEFCKKHLW
PMPTFDTSEE KSRTPFEFID GGEKRTSFSS FTSTITLRIP NREAVMYAGE ARPDKKSSFD
SAVVELLYEL ERRKIVIIQK
