Q3EBC8 (DCL2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Endoribonuclease Dicer homolog 2
EC=3.1.26.-

Alternative name(s):
Dicer-like protein 2
Short name=AtDCL2

Gene names

Ordered Locus Names:	At3g03300
ORF Names:	T17B22.1

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	1388 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS). Involved in the processing of natural small interfering RNAs (nat-siRNAs, derived from cis-natural antisense transcripts) by cleaving small dsRNAs into 24 nucleotide nat-siRNAs. Plays an essential role in transitive silencing of transgenes by processing secondary siRNAs. This pathway, which requires DCL4 and RDR6, amplifies silencing by using the target RNA as substrate to generate secondary siRNAs, providing an efficient mechanism for long-distance silencing. May participate with DCL3 in the production of 24 nucleotide repeat-associated siRNAs (ra-siRNAs) which derive from heterochromatin and DNA repeats such as transposons. Plays a role in antiviral RNA silencing. Involved in the production of viral siRNAs derived from the turnip crinkle virus (TCV) and tobacco rattle virus (TRV). Targeted by the viral silencing suppressor (VSR) protein 2b of the cucumber mosaic virus (CMV) that inactivates DCL2 function in RNA silencing. Does not seem to be involved in microRNAs (miRNAs) processing. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10
Cofactor	Magnesium or manganese By similarity.
Subcellular location	Nucleus. Cytoplasm Ref.4.
Sequence similarities	Belongs to the helicase family. Dicer subfamily. Contains 1 Dicer dsRNA-binding fold domain. Contains 1 DRBM (double-stranded RNA-binding) domain. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 PAZ domain. Contains 2 RNase III domains.
Sequence caution	The sequence AAF26098.1 differs from that shown. Reason: Erroneous gene model prediction. The predicted gene At3g03300 has been split into 2 genes: At3g03300 and At3g03305. The sequence ABF19797.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Plant defense RNA-mediated gene silencing
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding RNA-binding
Molecular function	Endonuclease Helicase Hydrolase Nuclease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	defense response to virus Inferred from mutant phenotype PubMed 16741077. Source: TAIR maintenance of DNA methylation Inferred from mutant phenotype PubMed 16699516. Source: TAIR nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC production of ta-siRNAs involved in RNA interference Inferred from mutant phenotype PubMed 16699516Ref.6. Source: TAIR
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro double-stranded RNA binding Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease III activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DRB1	O04492	2	EBI-2464030,EBI-632620

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q3EBC8-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q3EBC8-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-83: MTMDADAMET...VFLVPQVVLV → MLLCLLGSSS...IISAFFLVCF

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1388	1388	Endoribonuclease Dicer homolog 2		PRO_0000404660
Regions
	Domain	31 – 210	180	Helicase ATP-binding
	Domain	380 – 544	165	Helicase C-terminal
	Domain	559 – 645	87	Dicer dsRNA-binding fold
	Domain	807 – 935	129	PAZ
	Domain	962 – 1113	152	RNase III 1
	Domain	1149 – 1296	148	RNase III 2
	Domain	1315 – 1384	70	DRBM
	Nucleotide binding	44 – 51	8	ATP By similarity
	Motif	152 – 155	4	DECH box
Sites
	Metal binding	1188	1	Magnesium or manganese By similarity
	Metal binding	1282	1	Magnesium or manganese By similarity
	Metal binding	1285	1	Magnesium or manganese By similarity
	Site	1278	1	Important for activity By similarity
Natural variations
	Alternative sequence	1 – 83	83	MTMDA…QVVLV → MLLCLLGSSSGSCHSGIGVR IGVVDKGIHQYTDLSFVLQF LHYYTCSFSKFRNFSVTFSI ISAFFLVCF in isoform 2.		VSP_040615
Experimental info
	Sequence conflict	511	1	L → S in ABF19797. Ref.1
	Sequence conflict	511	1	L → S in ABF19798. Ref.1
	Sequence conflict	693	1	F → L in ABF19797. Ref.1
	Sequence conflict	693	1	F → L in ABF19798. Ref.1
	Sequence conflict	738	1	Q → R in ABF19797. Ref.1
	Sequence conflict	738	1	Q → R in ABF19798. Ref.1
	Sequence conflict	1130	1	F → L in ABF19797. Ref.1
	Sequence conflict	1130	1	F → L in ABF19798. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified January 15, 2008. Version 2. Checksum: 385D5A28E048B10D	FASTA	1,388	156,865
	10 20 30 40 50 60 MTMDADAMET ETTDQVSASP LHFARSYQVE ALEKAIKQNT IVFLETGSGK TLIAIMLLRS 70 80 90 100 110 120 YAYLFRKPSP CFCVFLVPQV VLVTQQAEAL KMHTDLKVGM YWGDMGVDFW DSSTWKQEVD 130 140 150 160 170 180 KYEVLVMTPA ILLDALRHSF LSLSMIKVLI VDECHHAGGK HPYACIMREF YHKELNSGTS 190 200 210 220 230 240 NVPRIFGMTA SLVKTKGENL DSYWKKIHEL ETLMNSKVYT CENESVLAGF VPFSTPSFKY 250 260 270 280 290 300 YQHIKIPSPK RASLVEKLER LTIKHRLSLG TLDLNSSTVD SVEKRLLRIS STLTYCLDDL 310 320 330 340 350 360 GILLAQKAAQ SLSASQNDSF LWGELNMFSV ALVKKFCSDA SQEFLAEIPQ GLNWSVANIN 370 380 390 400 410 420 GNAEAGLLTL KTVCLIETLL GYSSLENIRC IIFVDRVITA IVLESLLAEI LPNCNNWKTK 430 440 450 460 470 480 YVAGNNSGLQ NQTRKKQNEI VEDFRRGLVN IIVATSILEE GLDVQSCNLV IRFDPASNIC 490 500 510 520 530 540 SFIQSRGRAR MQNSDYLMMV ESGDLLTQSR LMKYLSGGKR MREESLDHSL VPCPPLPDDS 550 560 570 580 590 600 DEPLFRVEST GATVTLSSSV SLIYHYCSRL PSDEYFKPAP RFDVNKDQGS CTLYLPKSCP 610 620 630 640 650 660 VKEVKAEANN KVLKQAVCLK ACIQLHKVGA LSDHLVPDMV VAETVSQKLE KIQYNTEQPC 670 680 690 700 710 720 YFPPELVSQF SAQPETTYHF YLIRMKPNSP RNFHLNDVLL GTRVVLEDDI GNTSFRLEDH 730 740 750 760 770 780 RGTIAVTLSY VGAFHLTQEE VLFCRRFQIT LFRVLLDHSV ENLMEALNGL HLRDGVALDY 790 800 810 820 830 840 LLVPSTHSHE TSLIDWEVIR SVNLTSHEVL EKHENCSTNG ASRILHTKDG LFCTCVVQNA 850 860 870 880 890 900 LVYTPHNGYV YCTKGVLNNL NGNSLLTKRN SGDQTYIEYY EERHGIQLNF VDEPLLNGRH 910 920 930 940 950 960 IFTLHSYLHM AKKKKEKEHD REFVELPPEL CHVILSPISV DMIYSYTFIP SVMQRIESLL 970 980 990 1000 1010 1020 IAYNLKKSIP KVNIPTIKVL EAITTKKCED QFHLESLETL GDSFLKYAVC QQLFQHCHTH 1030 1040 1050 1060 1070 1080 HEGLLSTKKD GMISNVMLCQ FGCQQKLQGF IRDECFEPKG WMVPGQSSAA YSLVNDTLPE 1090 1100 1110 1120 1130 1140 SRNIYVASRR NLKRKSVADV VESLIGAYLS EGGELAALMF MNWVGIKVDF TTTKIQRDSP 1150 1160 1170 1180 1190 1200 IQAEKLVNVG YMESLLNYSF EDKSLLVEAL THGSYMMPEI PRCYQRLEFL GDSVLDYLIT 1210 1220 1230 1240 1250 1260 KHLYDKYPCL SPGLLTDMRS ASVNNECYAL VAVKANLHKH ILYASHHLHK HISRTVSEFE 1270 1280 1290 1300 1310 1320 QSSLQSTFGW ESDISFPKVL GDVIESLAGA IFVDSGYNKE VVFASIKPLL GCMITPETVK 1330 1340 1350 1360 1370 1380 LHPVRELTEL CQKWQFELSK AKDFDSFTVE VKAKEMSFAH TAKASDKKMA KKLAYKEVLN LLKNSLDY
	Isoform 2 [UniParc]. Checksum: 8A374D2F3B727D53	FASTA	1,374	155,286
	10 20 30 40 50 60 MLLCLLGSSS GSCHSGIGVR IGVVDKGIHQ YTDLSFVLQF LHYYTCSFSK FRNFSVTFSI 70 80 90 100 110 120 ISAFFLVCFT QQAEALKMHT DLKVGMYWGD MGVDFWDSST WKQEVDKYEV LVMTPAILLD 130 140 150 160 170 180 ALRHSFLSLS MIKVLIVDEC HHAGGKHPYA CIMREFYHKE LNSGTSNVPR IFGMTASLVK 190 200 210 220 230 240 TKGENLDSYW KKIHELETLM NSKVYTCENE SVLAGFVPFS TPSFKYYQHI KIPSPKRASL 250 260 270 280 290 300 VEKLERLTIK HRLSLGTLDL NSSTVDSVEK RLLRISSTLT YCLDDLGILL AQKAAQSLSA 310 320 330 340 350 360 SQNDSFLWGE LNMFSVALVK KFCSDASQEF LAEIPQGLNW SVANINGNAE AGLLTLKTVC 370 380 390 400 410 420 LIETLLGYSS LENIRCIIFV DRVITAIVLE SLLAEILPNC NNWKTKYVAG NNSGLQNQTR 430 440 450 460 470 480 KKQNEIVEDF RRGLVNIIVA TSILEEGLDV QSCNLVIRFD PASNICSFIQ SRGRARMQNS 490 500 510 520 530 540 DYLMMVESGD LLTQSRLMKY LSGGKRMREE SLDHSLVPCP PLPDDSDEPL FRVESTGATV 550 560 570 580 590 600 TLSSSVSLIY HYCSRLPSDE YFKPAPRFDV NKDQGSCTLY LPKSCPVKEV KAEANNKVLK 610 620 630 640 650 660 QAVCLKACIQ LHKVGALSDH LVPDMVVAET VSQKLEKIQY NTEQPCYFPP ELVSQFSAQP 670 680 690 700 710 720 ETTYHFYLIR MKPNSPRNFH LNDVLLGTRV VLEDDIGNTS FRLEDHRGTI AVTLSYVGAF 730 740 750 760 770 780 HLTQEEVLFC RRFQITLFRV LLDHSVENLM EALNGLHLRD GVALDYLLVP STHSHETSLI 790 800 810 820 830 840 DWEVIRSVNL TSHEVLEKHE NCSTNGASRI LHTKDGLFCT CVVQNALVYT PHNGYVYCTK 850 860 870 880 890 900 GVLNNLNGNS LLTKRNSGDQ TYIEYYEERH GIQLNFVDEP LLNGRHIFTL HSYLHMAKKK 910 920 930 940 950 960 KEKEHDREFV ELPPELCHVI LSPISVDMIY SYTFIPSVMQ RIESLLIAYN LKKSIPKVNI 970 980 990 1000 1010 1020 PTIKVLEAIT TKKCEDQFHL ESLETLGDSF LKYAVCQQLF QHCHTHHEGL LSTKKDGMIS 1030 1040 1050 1060 1070 1080 NVMLCQFGCQ QKLQGFIRDE CFEPKGWMVP GQSSAAYSLV NDTLPESRNI YVASRRNLKR 1090 1100 1110 1120 1130 1140 KSVADVVESL IGAYLSEGGE LAALMFMNWV GIKVDFTTTK IQRDSPIQAE KLVNVGYMES 1150 1160 1170 1180 1190 1200 LLNYSFEDKS LLVEALTHGS YMMPEIPRCY QRLEFLGDSV LDYLITKHLY DKYPCLSPGL 1210 1220 1230 1240 1250 1260 LTDMRSASVN NECYALVAVK ANLHKHILYA SHHLHKHISR TVSEFEQSSL QSTFGWESDI 1270 1280 1290 1300 1310 1320 SFPKVLGDVI ESLAGAIFVD SGYNKEVVFA SIKPLLGCMI TPETVKLHPV RELTELCQKW 1330 1340 1350 1360 1370 QFELSKAKDF DSFTVEVKAK EMSFAHTAKA SDKKMAKKLA YKEVLNLLKN SLDY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The evolution and diversification of Dicers in plants." Margis R., Fusaro A.F., Smith N.A., Curtin S.J., Watson J.M., Finnegan E.J., Waterhouse P.M. FEBS Lett. 580:2442-2450(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
[2]	"Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana." Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F. , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S. Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Genetic and functional diversification of small RNA pathways in plants." Xie Z., Johansen L.K., Gustafson A.M., Kasschau K.D., Lellis A.D., Zilberman D., Jacobsen S.E., Carrington J.C. PLoS Biol. 2:E104-E104(2004) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[5]	"Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs." Gasciolli V., Mallory A.C., Bartel D.P., Vaucheret H. Curr. Biol. 15:1494-1500(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs." Bouche N., Lauressergues D., Gasciolli V., Vaucheret H. EMBO J. 25:3347-3356(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs." Diaz-Pendon J.A., Li F., Li W.X., Ding S.W. Plant Cell 19:2053-2063(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins." Moissiard G., Parizotto E.A., Himber C., Voinnet O. RNA 13:1268-1278(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs." Donaire L., Barajas D., Martinez-Garcia B., Martinez-Priego L., Pagan I., Llave C. J. Virol. 82:5167-5177(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis." Mlotshwa S., Pruss G.J., Peragine A., Endres M.W., Li J., Chen X., Poethig R.S., Bowman L.H., Vance V. PLoS ONE 3:E1755-E1755(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	DQ479970 mRNA. Translation: ABF19797.1. Different initiation. DQ479971 mRNA. Translation: ABF19798.1. AC012328 Genomic DNA. Translation: AAF26098.1. Sequence problems. CP002686 Genomic DNA. Translation: AEE73924.1. CP002686 Genomic DNA. Translation: AEE73925.1. CP002686 Genomic DNA. Translation: AEE73926.1.
IPI	IPI00530074. IPI00852241.
RefSeq	NP_001078101.1. NM_001084632.1. NP_001189798.1. NM_001202869.1. NP_566199.4. NM_111200.5.
UniGene	At.43488.
3D structure databases
ProteinModelPortal	Q3EBC8.
SMR	Q3EBC8. Positions 11-638, 1152-1385.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q3EBC8. 4 interactions.
STRING	3702.AT3G03300.1-P.
Proteomic databases
PaxDb	Q3EBC8.
PRIDE	Q3EBC8.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT3G03300.1; AT3G03300.1; AT3G03300. AT3G03300.3; AT3G03300.3; AT3G03300.
GeneID	821300.
KEGG	ath:AT3G03300.
Organism-specific databases
TAIR	At3g03300.
Phylogenomic databases
eggNOG	COG1111.
HOGENOM	HOG000006099.
InParanoid	Q3EBC8.
KO	K11592.
OMA	TAIVLES.
PhylomeDB	Q3EBC8.
ProtClustDB	CLSN2694055.
Gene expression databases
Genevestigator	Q3EBC8.
Family and domain databases
Gene3D	1.10.1520.10. 2 hits.
InterPro	IPR005034. Dicer_dsRNA_binding_fold. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR001159. Ds-RNA-bd. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR027417. P-loop_NTPase. IPR003100. PAZ. IPR000999. RNase_III_dom. [Graphical view]
Pfam	PF00270. DEAD. 1 hit. PF03368. dsRNA_bind. 1 hit. PF00271. Helicase_C. 1 hit. PF02170. PAZ. 1 hit. PF00636. Ribonuclease_3. 2 hits. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00358. DSRM. 1 hit. SM00490. HELICc. 1 hit. SM00949. PAZ. 1 hit. SM00535. RIBOc. 2 hits. [Graphical view]
SUPFAM	SSF101690. PAZ. 1 hit. SSF69065. RNase_III. 2 hits. SSF52540. SSF52540. 1 hit.
PROSITE	PS51327. DICER_DSRBF. 1 hit. PS50137. DS_RBD. 1 hit. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS50821. PAZ. 1 hit. PS00517. RNASE_3_1. 1 hit. PS50142. RNASE_3_2. 2 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DCL2_ARATH

Accession

Primary (citable) accession number: Q3EBC8
Secondary accession number(s): Q1KL57, Q1KL58, Q9M9P8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 8, 2011
Last sequence update:	January 15, 2008
Last modified:	May 29, 2013
This is version 69 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program