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Q3EBC8 (DCL2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length1388 AA.
Sequence statusComplete.
Protein existenceEvidence 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.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

DRB1O044922EBI-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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 13881388Endoribonuclease Dicer homolog 2
PRO_0000404660

Regions

Domain31 – 210180Helicase ATP-binding
Domain380 – 544165Helicase C-terminal
Domain559 – 64587Dicer dsRNA-binding fold
Domain807 – 935129PAZ
Domain962 – 1113152RNase III 1
Domain1149 – 1296148RNase III 2
Domain1315 – 138470DRBM
Nucleotide binding44 – 518ATP By similarity
Motif152 – 1554DECH box

Sites

Metal binding11881Magnesium or manganese By similarity
Metal binding12821Magnesium or manganese By similarity
Metal binding12851Magnesium or manganese By similarity
Site12781Important for activity By similarity

Natural variations

Alternative sequence1 – 8383MTMDA…QVVLV → MLLCLLGSSSGSCHSGIGVR IGVVDKGIHQYTDLSFVLQF LHYYTCSFSKFRNFSVTFSI ISAFFLVCF in isoform 2.
VSP_040615

Experimental info

Sequence conflict5111L → S in ABF19797. Ref.1
Sequence conflict5111L → S in ABF19798. Ref.1
Sequence conflict6931F → L in ABF19797. Ref.1
Sequence conflict6931F → L in ABF19798. Ref.1
Sequence conflict7381Q → R in ABF19797. Ref.1
Sequence conflict7381Q → R in ABF19798. Ref.1
Sequence conflict11301F → L in ABF19797. Ref.1
Sequence conflict11301F → L in ABF19798. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified January 15, 2008. Version 2.
Checksum: 385D5A28E048B10D

FASTA1,388156,865
        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 

« Hide

Isoform 2 [UniParc].

Checksum: 8A374D2F3B727D53
Show »

FASTA1,374155,286

References

« Hide '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. expand/collapse author list , 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.
RefSeqNP_001078101.1. NM_001084632.1.
NP_001189798.1. NM_001202869.1.
NP_566199.4. NM_111200.5.
UniGeneAt.43488.

3D structure databases

ProteinModelPortalQ3EBC8.
SMRQ3EBC8. Positions 11-638, 836-933, 982-1124, 1147-1384.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ3EBC8. 4 interactions.
STRING3702.AT3G03300.1-P.

Proteomic databases

PaxDbQ3EBC8.
PRIDEQ3EBC8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT3G03300.1; AT3G03300.1; AT3G03300. [Q3EBC8-1]
AT3G03300.3; AT3G03300.3; AT3G03300. [Q3EBC8-1]
GeneID821300.
KEGGath:AT3G03300.

Organism-specific databases

TAIRAT3G03300.

Phylogenomic databases

eggNOGCOG1111.
HOGENOMHOG000006099.
InParanoidQ3EBC8.
KOK11592.
OMAHPYACIM.
PhylomeDBQ3EBC8.
ProtClustDBCLSN2694055.

Enzyme and pathway databases

BioCycARA:AT3G03300-MONOMER.
ARA:GQT-1567-MONOMER.

Gene expression databases

GenevestigatorQ3EBC8.

Family and domain databases

Gene3D1.10.1520.10. 2 hits.
3.40.50.300. 2 hits.
InterProIPR005034. Dicer_dimerisation_dom.
IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014720. dsRNA-bd_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR003100. PAZ_dom.
IPR000999. RNase_III_dom.
[Graphical view]
PfamPF00270. DEAD. 1 hit.
PF03368. Dicer_dimer. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF00636. Ribonuclease_3. 2 hits.
[Graphical view]
SMARTSM00487. DEXDc. 1 hit.
SM00358. DSRM. 1 hit.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]
SUPFAMSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 4 hits.
PROSITEPS51327. 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]
ProtoNetSearch...

Entry information

Entry nameDCL2_ARATH
AccessionPrimary (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: April 16, 2014
This is version 78 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names