GenomeNet

Database: UniProt
Entry: Q3EBC8
LinkDB: Q3EBC8
Original site: Q3EBC8 
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   16-OCT-2019, entry version 117.
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;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   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.,
RA   Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B.,
RA   Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P.,
RA   De Simone V., Choisne N., Artiguenave F., Robert C., Brottier P.,
RA   Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F.,
RA   Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V.,
RA   Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S.,
RA   Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G.,
RA   Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B.,
RA   Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G.,
RA   Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J.,
RA   Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D.,
RA   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.,
RA   Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W.,
RA   Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J.,
RA   Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P.,
RA   Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S.,
RA   Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V.,
RA   Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C.,
RA   Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E.,
RA   Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y.,
RA   Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A.,
RA   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
RT   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
RT   reference 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
RT   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
RT   role 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
RT   new 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
RT   protein in Arabidopsis is associated with drastically reduced
RT   accumulation of three 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
RT   action of the antiviral Dicer-like 4 and Dicer-like 2, and is
RT   compromised by 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.,
RA   Pagan I., Llave C.;
RT   "Structural and genetic requirements for the biogenesis of tobacco
RT   rattle 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
RT   transgenes in 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
RT   family in Zea mays and Glycine max: a comparison with Arabidopsis and
RT   Oryza 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
CC       of natural small interfering RNAs (nat-siRNAs, derived from cis-
CC       natural antisense transcripts) by cleaving small dsRNAs into 24
CC       nucleotide nat-siRNAs. Plays an essential role in transitive
CC       silencing of transgenes by processing secondary siRNAs. This
CC       pathway, which requires DCL4 and RDR6, amplifies silencing by
CC       using the target RNA as substrate to generate secondary siRNAs,
CC       providing an efficient mechanism for long-distance silencing. May
CC       participate with DCL3 in the production of 24 nucleotide repeat-
CC       associated siRNAs (ra-siRNAs) which derive from heterochromatin
CC       and DNA repeats such as transposons. Plays a role in antiviral RNA
CC       silencing. Involved in the production of viral siRNAs derived from
CC       the turnip crinkle virus (TCV) and tobacco rattle virus (TRV).
CC       Targeted by the viral silencing suppressor (VSR) protein 2b of the
CC       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,
CC       ECO:0000269|PubMed:16810317, ECO:0000269|PubMed:17586651,
CC       ECO:0000269|PubMed:17592042, ECO:0000269|PubMed:18335032,
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   -!- INTERACTION:
CC       O04492:DRB1; NbExp=2; IntAct=EBI-2464030, EBI-632620;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15024409}.
CC       Cytoplasm {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         Note=No experimental confirmation available.;
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};
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   IntAct; Q3EBC8; 4.
DR   STRING; 3702.AT3G03300.1; -.
DR   iPTMnet; Q3EBC8; -.
DR   PaxDb; Q3EBC8; -.
DR   PRIDE; Q3EBC8; -.
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   eggNOG; COG0571; LUCA.
DR   eggNOG; COG1111; LUCA.
DR   HOGENOM; HOG000006099; -.
DR   InParanoid; Q3EBC8; -.
DR   KO; K11592; -.
DR   OMA; PTVALCE; -.
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:0016442; C:RISC complex; 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; IEA:UniProtKB-KW.
DR   GO; GO:0010216; P:maintenance of DNA methylation; IMP:TAIR.
DR   GO; GO:0030422; P:production of siRNA involved in RNA interference; IBA:GO_Central.
DR   GO; GO:0010267; P:production of ta-siRNAs involved in RNA interference; IMP:TAIR.
DR   GO; GO:0051214; P:RNA virus induced gene silencing; IGI:TAIR.
DR   CDD; cd00593; RIBOc; 2.
DR   Gene3D; 1.10.1520.10; -; 2.
DR   Gene3D; 3.30.160.380; -; 1.
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; PF03368; Dicer_dimer; 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; Complete proteome; Cytoplasm;
KW   Endonuclease; Helicase; Hydrolase; Magnesium; Manganese;
KW   Metal-binding; Nuclease; Nucleotide-binding; Nucleus; Plant defense;
KW   Reference proteome; Repeat; RNA-binding; RNA-mediated gene silencing.
FT   CHAIN         1   1388       Endoribonuclease Dicer homolog 2.
FT                                /FTId=PRO_0000404660.
FT   DOMAIN       31    210       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      380    544       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   DOMAIN      559    645       Dicer dsRNA-binding fold.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00657}.
FT   DOMAIN      807    935       PAZ. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00142}.
FT   DOMAIN      962   1113       RNase III 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00177}.
FT   DOMAIN     1149   1296       RNase III 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00177}.
FT   DOMAIN     1315   1384       DRBM. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00266}.
FT   NP_BIND      44     51       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF       152    155       DECH box.
FT   METAL      1188   1188       Magnesium or manganese. {ECO:0000250}.
FT   METAL      1282   1282       Magnesium or manganese. {ECO:0000250}.
FT   METAL      1285   1285       Magnesium or manganese. {ECO:0000250}.
FT   SITE       1278   1278       Important for activity. {ECO:0000250}.
FT   VAR_SEQ       1     83       MTMDADAMETETTDQVSASPLHFARSYQVEALEKAIKQNTI
FT                                VFLETGSGKTLIAIMLLRSYAYLFRKPSPCFCVFLVPQVVL
FT                                V -> MLLCLLGSSSGSCHSGIGVRIGVVDKGIHQYTDLSF
FT                                VLQFLHYYTCSFSKFRNFSVTFSIISAFFLVCF (in
FT                                isoform 2).
FT                                {ECO:0000303|PubMed:16638569}.
FT                                /FTId=VSP_040615.
FT   CONFLICT    511    511       L -> S (in Ref. 1; ABF19797/ABF19798).
FT                                {ECO:0000305}.
FT   CONFLICT    693    693       F -> L (in Ref. 1; ABF19797/ABF19798).
FT                                {ECO:0000305}.
FT   CONFLICT    738    738       Q -> R (in Ref. 1; ABF19797/ABF19798).
FT                                {ECO:0000305}.
FT   CONFLICT   1130   1130       F -> L (in Ref. 1; ABF19797/ABF19798).
FT                                {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
//
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