DCL2_ARATH
ID DCL2_ARATH Reviewed; 1388 AA.
AC Q3EBC8; Q1KL57; Q1KL58; Q9M9P8;
DT 08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Endoribonuclease Dicer homolog 2;
DE EC=3.1.26.-;
DE AltName: Full=Dicer-like protein 2;
DE Short=AtDCL2;
GN OrderedLocusNames=At3g03300; ORFNames=T17B22.1;
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] (ISOFORMS 1 AND 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 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 [7]
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 [8]
RP FUNCTION.
RX PubMed=17592042; DOI=10.1261/rna.541307;
RA Moissiard G., Parizotto E.A., Himber C., Voinnet O.;
RT "Transitivity in Arabidopsis can be primed, requires the redundant action
RT of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by
RT viral-encoded suppressor proteins.";
RL RNA 13:1268-1278(2007).
RN [9]
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 [10]
RP FUNCTION.
RX PubMed=18335032; DOI=10.1371/journal.pone.0001755;
RA Mlotshwa S., Pruss G.J., Peragine A., Endres M.W., Li J., Chen X.,
RA Poethig R.S., Bowman L.H., Vance V.;
RT "DICER-LIKE2 plays a primary role in transitive silencing of transgenes in
RT Arabidopsis.";
RL PLoS ONE 3:E1755-E1755(2008).
RN [11]
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 natural small interfering RNAs (nat-siRNAs, derived from cis-natural
CC antisense transcripts) by cleaving small dsRNAs into 24 nucleotide nat-
CC siRNAs. Plays an essential role in transitive silencing of transgenes
CC by processing secondary siRNAs. This pathway, which requires DCL4 and
CC RDR6, amplifies silencing by using the target RNA as substrate to
CC generate secondary siRNAs, providing an efficient mechanism for long-
CC distance silencing. May participate with DCL3 in the production of 24
CC nucleotide repeat-associated siRNAs (ra-siRNAs) which derive from
CC heterochromatin and DNA repeats such as transposons. Plays a role in
CC antiviral RNA silencing. Involved in the production of viral siRNAs
CC derived from the turnip crinkle virus (TCV) and tobacco rattle virus
CC (TRV). Targeted by the viral silencing suppressor (VSR) protein 2b of
CC the cucumber mosaic virus (CMV) that inactivates DCL2 function in RNA
CC silencing. Does not seem to be involved in microRNAs (miRNAs)
CC processing. {ECO:0000269|PubMed:16040244, ECO:0000269|PubMed:16810317,
CC ECO:0000269|PubMed:17586651, ECO:0000269|PubMed:17592042,
CC ECO:0000269|PubMed:18335032, 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 -!- INTERACTION:
CC Q3EBC8; O04492: DRB1; NbExp=2; IntAct=EBI-2464030, EBI-632620;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15024409}. Cytoplasm
CC {ECO:0000269|PubMed:15024409}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q3EBC8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q3EBC8-2; Sequence=VSP_040615;
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00657}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF26098.1; Type=Erroneous gene model prediction; Note=The predicted gene At3g03300 has been split into 2 genes: At3g03300 and At3g03305.; Evidence={ECO:0000305};
CC Sequence=ABF19797.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; DQ479970; ABF19797.1; ALT_INIT; mRNA.
DR EMBL; DQ479971; ABF19798.1; -; mRNA.
DR EMBL; AC012328; AAF26098.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE73924.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73925.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73926.1; -; Genomic_DNA.
DR RefSeq; NP_001078101.1; NM_001084632.1. [Q3EBC8-2]
DR RefSeq; NP_001189798.1; NM_001202869.2. [Q3EBC8-1]
DR RefSeq; NP_566199.4; NM_111200.5. [Q3EBC8-1]
DR AlphaFoldDB; Q3EBC8; -.
DR SMR; Q3EBC8; -.
DR IntAct; Q3EBC8; 4.
DR STRING; 3702.AT3G03300.1; -.
DR iPTMnet; Q3EBC8; -.
DR PaxDb; Q3EBC8; -.
DR PRIDE; Q3EBC8; -.
DR ProteomicsDB; 224607; -. [Q3EBC8-1]
DR EnsemblPlants; AT3G03300.1; AT3G03300.1; AT3G03300. [Q3EBC8-1]
DR EnsemblPlants; AT3G03300.2; AT3G03300.2; AT3G03300. [Q3EBC8-2]
DR EnsemblPlants; AT3G03300.3; AT3G03300.3; AT3G03300. [Q3EBC8-1]
DR GeneID; 821300; -.
DR Gramene; AT3G03300.1; AT3G03300.1; AT3G03300. [Q3EBC8-1]
DR Gramene; AT3G03300.2; AT3G03300.2; AT3G03300. [Q3EBC8-2]
DR Gramene; AT3G03300.3; AT3G03300.3; AT3G03300. [Q3EBC8-1]
DR KEGG; ath:AT3G03300; -.
DR Araport; AT3G03300; -.
DR TAIR; locus:2097705; AT3G03300.
DR eggNOG; KOG0701; Eukaryota.
DR HOGENOM; CLU_000907_4_4_1; -.
DR InParanoid; Q3EBC8; -.
DR OMA; HFCAVIP; -.
DR OrthoDB; 1337630at2759; -.
DR PhylomeDB; Q3EBC8; -.
DR PRO; PR:Q3EBC8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q3EBC8; baseline and differential.
DR Genevisible; Q3EBC8; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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; IBA:GO_Central.
DR GO; GO:0010267; P:ta-siRNA processing; IMP:TAIR.
DR CDD; cd00593; RIBOc; 2.
DR Gene3D; 1.10.1520.10; -; 2.
DR Gene3D; 3.30.160.380; -; 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; 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 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Cytoplasm; Endonuclease; Helicase;
KW Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease;
KW Nucleotide-binding; Nucleus; Plant defense; Reference proteome; Repeat;
KW RNA-binding; RNA-mediated gene silencing.
FT CHAIN 1..1388
FT /note="Endoribonuclease Dicer homolog 2"
FT /id="PRO_0000404660"
FT DOMAIN 31..210
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 380..544
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 559..645
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 807..935
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 962..1113
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1149..1296
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1315..1384
FT /note="DRBM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT MOTIF 152..155
FT /note="DECH box"
FT BINDING 44..51
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1188
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1282
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1285
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1278
FT /note="Important for activity"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..83
FT /note="MTMDADAMETETTDQVSASPLHFARSYQVEALEKAIKQNTIVFLETGSGKTL
FT IAIMLLRSYAYLFRKPSPCFCVFLVPQVVLV -> MLLCLLGSSSGSCHSGIGVRIGVV
FT DKGIHQYTDLSFVLQFLHYYTCSFSKFRNFSVTFSIISAFFLVCF (in isoform
FT 2)"
FT /evidence="ECO:0000303|PubMed:16638569"
FT /id="VSP_040615"
FT CONFLICT 511
FT /note="L -> S (in Ref. 1; ABF19797/ABF19798)"
FT /evidence="ECO:0000305"
FT CONFLICT 693
FT /note="F -> L (in Ref. 1; ABF19797/ABF19798)"
FT /evidence="ECO:0000305"
FT CONFLICT 738
FT /note="Q -> R (in Ref. 1; ABF19797/ABF19798)"
FT /evidence="ECO:0000305"
FT CONFLICT 1130
FT /note="F -> L (in Ref. 1; ABF19797/ABF19798)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1388 AA; 156865 MW; 385D5A28E048B10D CRC64;
MTMDADAMET ETTDQVSASP LHFARSYQVE ALEKAIKQNT IVFLETGSGK TLIAIMLLRS
YAYLFRKPSP CFCVFLVPQV VLVTQQAEAL KMHTDLKVGM YWGDMGVDFW DSSTWKQEVD
KYEVLVMTPA ILLDALRHSF LSLSMIKVLI VDECHHAGGK HPYACIMREF YHKELNSGTS
NVPRIFGMTA SLVKTKGENL DSYWKKIHEL ETLMNSKVYT CENESVLAGF VPFSTPSFKY
YQHIKIPSPK RASLVEKLER LTIKHRLSLG TLDLNSSTVD SVEKRLLRIS STLTYCLDDL
GILLAQKAAQ SLSASQNDSF LWGELNMFSV ALVKKFCSDA SQEFLAEIPQ GLNWSVANIN
GNAEAGLLTL KTVCLIETLL GYSSLENIRC IIFVDRVITA IVLESLLAEI LPNCNNWKTK
YVAGNNSGLQ NQTRKKQNEI VEDFRRGLVN IIVATSILEE GLDVQSCNLV IRFDPASNIC
SFIQSRGRAR MQNSDYLMMV ESGDLLTQSR LMKYLSGGKR MREESLDHSL VPCPPLPDDS
DEPLFRVEST GATVTLSSSV SLIYHYCSRL PSDEYFKPAP RFDVNKDQGS CTLYLPKSCP
VKEVKAEANN KVLKQAVCLK ACIQLHKVGA LSDHLVPDMV VAETVSQKLE KIQYNTEQPC
YFPPELVSQF SAQPETTYHF YLIRMKPNSP RNFHLNDVLL GTRVVLEDDI GNTSFRLEDH
RGTIAVTLSY VGAFHLTQEE VLFCRRFQIT LFRVLLDHSV ENLMEALNGL HLRDGVALDY
LLVPSTHSHE TSLIDWEVIR SVNLTSHEVL EKHENCSTNG ASRILHTKDG LFCTCVVQNA
LVYTPHNGYV YCTKGVLNNL NGNSLLTKRN SGDQTYIEYY EERHGIQLNF VDEPLLNGRH
IFTLHSYLHM AKKKKEKEHD REFVELPPEL CHVILSPISV DMIYSYTFIP SVMQRIESLL
IAYNLKKSIP KVNIPTIKVL EAITTKKCED QFHLESLETL GDSFLKYAVC QQLFQHCHTH
HEGLLSTKKD GMISNVMLCQ FGCQQKLQGF IRDECFEPKG WMVPGQSSAA YSLVNDTLPE
SRNIYVASRR NLKRKSVADV VESLIGAYLS EGGELAALMF MNWVGIKVDF TTTKIQRDSP
IQAEKLVNVG YMESLLNYSF EDKSLLVEAL THGSYMMPEI PRCYQRLEFL GDSVLDYLIT
KHLYDKYPCL SPGLLTDMRS ASVNNECYAL VAVKANLHKH ILYASHHLHK HISRTVSEFE
QSSLQSTFGW ESDISFPKVL GDVIESLAGA IFVDSGYNKE VVFASIKPLL GCMITPETVK
LHPVRELTEL CQKWQFELSK AKDFDSFTVE VKAKEMSFAH TAKASDKKMA KKLAYKEVLN
LLKNSLDY
