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Q3EBC8

- DCL2_ARATH

UniProt

Q3EBC8 - DCL2_ARATH

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Protein

Endoribonuclease Dicer homolog 2

Gene
At3g03300, T17B22.1
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.6 Publications

Cofactori

Magnesium or manganese By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1188 – 11881Magnesium or manganese By similarity
Sitei1278 – 12781Important for activity By similarity
Metal bindingi1282 – 12821Magnesium or manganese By similarity
Metal bindingi1285 – 12851Magnesium or manganese By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi44 – 518ATP By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. helicase activity Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. protein binding Source: IntAct
  5. ribonuclease III activity Source: InterPro
  6. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. defense response to virus Source: TAIR
  2. maintenance of DNA methylation Source: TAIR
  3. production of ta-siRNAs involved in RNA interference Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Helicase, Hydrolase, Nuclease

Keywords - Biological processi

Plant defense, RNA-mediated gene silencing

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease Dicer homolog 2 (EC:3.1.26.-)
Alternative name(s):
Dicer-like protein 2
Short name:
AtDCL2
Gene namesi
Ordered Locus Names:At3g03300
ORF Names:T17B22.1
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 3

Organism-specific databases

TAIRiAT3G03300.

Subcellular locationi

Nucleus. Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 13881388Endoribonuclease Dicer homolog 2PRO_0000404660Add
BLAST

Proteomic databases

PaxDbiQ3EBC8.
PRIDEiQ3EBC8.

Expressioni

Gene expression databases

GenevestigatoriQ3EBC8.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
DRB1O044922EBI-2464030,EBI-632620

Protein-protein interaction databases

IntActiQ3EBC8. 4 interactions.
STRINGi3702.AT3G03300.1-P.

Structurei

3D structure databases

ProteinModelPortaliQ3EBC8.
SMRiQ3EBC8. Positions 11-510, 558-638, 1152-1385.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 210180Helicase ATP-bindingAdd
BLAST
Domaini380 – 544165Helicase C-terminalAdd
BLAST
Domaini559 – 64587Dicer dsRNA-binding foldAdd
BLAST
Domaini807 – 935129PAZAdd
BLAST
Domaini962 – 1113152RNase III 1Add
BLAST
Domaini1149 – 1296148RNase III 2Add
BLAST
Domaini1315 – 138470DRBMAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi152 – 1554DECH box

Sequence similaritiesi

Contains 1 PAZ domain.
Contains 2 RNase III domains.

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1111.
HOGENOMiHOG000006099.
InParanoidiQ3EBC8.
KOiK11592.
OMAiHILHASH.
PhylomeDBiQ3EBC8.

Family and domain databases

Gene3Di1.10.1520.10. 2 hits.
3.40.50.300. 2 hits.
InterProiIPR005034. 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]
PfamiPF00270. DEAD. 1 hit.
PF03368. Dicer_dimer. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF00636. Ribonuclease_3. 2 hits.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00358. DSRM. 1 hit.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 4 hits.
PROSITEiPS51327. 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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q3EBC8-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MTMDADAMET ETTDQVSASP LHFARSYQVE ALEKAIKQNT IVFLETGSGK     50
TLIAIMLLRS YAYLFRKPSP CFCVFLVPQV VLVTQQAEAL KMHTDLKVGM 100
YWGDMGVDFW DSSTWKQEVD KYEVLVMTPA ILLDALRHSF LSLSMIKVLI 150
VDECHHAGGK HPYACIMREF YHKELNSGTS NVPRIFGMTA SLVKTKGENL 200
DSYWKKIHEL ETLMNSKVYT CENESVLAGF VPFSTPSFKY YQHIKIPSPK 250
RASLVEKLER LTIKHRLSLG TLDLNSSTVD SVEKRLLRIS STLTYCLDDL 300
GILLAQKAAQ SLSASQNDSF LWGELNMFSV ALVKKFCSDA SQEFLAEIPQ 350
GLNWSVANIN GNAEAGLLTL KTVCLIETLL GYSSLENIRC IIFVDRVITA 400
IVLESLLAEI LPNCNNWKTK YVAGNNSGLQ NQTRKKQNEI VEDFRRGLVN 450
IIVATSILEE GLDVQSCNLV IRFDPASNIC SFIQSRGRAR MQNSDYLMMV 500
ESGDLLTQSR LMKYLSGGKR MREESLDHSL VPCPPLPDDS DEPLFRVEST 550
GATVTLSSSV SLIYHYCSRL PSDEYFKPAP RFDVNKDQGS CTLYLPKSCP 600
VKEVKAEANN KVLKQAVCLK ACIQLHKVGA LSDHLVPDMV VAETVSQKLE 650
KIQYNTEQPC YFPPELVSQF SAQPETTYHF YLIRMKPNSP RNFHLNDVLL 700
GTRVVLEDDI GNTSFRLEDH RGTIAVTLSY VGAFHLTQEE VLFCRRFQIT 750
LFRVLLDHSV ENLMEALNGL HLRDGVALDY LLVPSTHSHE TSLIDWEVIR 800
SVNLTSHEVL EKHENCSTNG ASRILHTKDG LFCTCVVQNA LVYTPHNGYV 850
YCTKGVLNNL NGNSLLTKRN SGDQTYIEYY EERHGIQLNF VDEPLLNGRH 900
IFTLHSYLHM AKKKKEKEHD REFVELPPEL CHVILSPISV DMIYSYTFIP 950
SVMQRIESLL IAYNLKKSIP KVNIPTIKVL EAITTKKCED QFHLESLETL 1000
GDSFLKYAVC QQLFQHCHTH HEGLLSTKKD GMISNVMLCQ FGCQQKLQGF 1050
IRDECFEPKG WMVPGQSSAA YSLVNDTLPE SRNIYVASRR NLKRKSVADV 1100
VESLIGAYLS EGGELAALMF MNWVGIKVDF TTTKIQRDSP IQAEKLVNVG 1150
YMESLLNYSF EDKSLLVEAL THGSYMMPEI PRCYQRLEFL GDSVLDYLIT 1200
KHLYDKYPCL SPGLLTDMRS ASVNNECYAL VAVKANLHKH ILYASHHLHK 1250
HISRTVSEFE QSSLQSTFGW ESDISFPKVL GDVIESLAGA IFVDSGYNKE 1300
VVFASIKPLL GCMITPETVK LHPVRELTEL CQKWQFELSK AKDFDSFTVE 1350
VKAKEMSFAH TAKASDKKMA KKLAYKEVLN LLKNSLDY 1388
Length:1,388
Mass (Da):156,865
Last modified:January 15, 2008 - v2
Checksum:i385D5A28E048B10D
GO
Isoform 2 (identifier: Q3EBC8-2) [UniParc]FASTAAdd to Basket

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

Note: No experimental confirmation available.

Show »
Length:1,374
Mass (Da):155,286
Checksum:i8A374D2F3B727D53
GO

Sequence cautioni

The sequence ABF19797.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
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.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 8383MTMDA…QVVLV → MLLCLLGSSSGSCHSGIGVR IGVVDKGIHQYTDLSFVLQF LHYYTCSFSKFRNFSVTFSI ISAFFLVCF in isoform 2. VSP_040615Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti511 – 5111L → S in ABF19797. 1 Publication
Sequence conflicti511 – 5111L → S in ABF19798. 1 Publication
Sequence conflicti693 – 6931F → L in ABF19797. 1 Publication
Sequence conflicti693 – 6931F → L in ABF19798. 1 Publication
Sequence conflicti738 – 7381Q → R in ABF19797. 1 Publication
Sequence conflicti738 – 7381Q → R in ABF19798. 1 Publication
Sequence conflicti1130 – 11301F → L in ABF19797. 1 Publication
Sequence conflicti1130 – 11301F → L in ABF19798. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
RefSeqiNP_001078101.1. NM_001084632.1. [Q3EBC8-2]
NP_001189798.1. NM_001202869.1. [Q3EBC8-1]
NP_566199.4. NM_111200.5. [Q3EBC8-1]
UniGeneiAt.43488.

Genome annotation databases

EnsemblPlantsiAT3G03300.1; AT3G03300.1; AT3G03300. [Q3EBC8-1]
AT3G03300.3; AT3G03300.3; AT3G03300. [Q3EBC8-1]
GeneIDi821300.
KEGGiath:AT3G03300.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
RefSeqi NP_001078101.1. NM_001084632.1. [Q3EBC8-2 ]
NP_001189798.1. NM_001202869.1. [Q3EBC8-1 ]
NP_566199.4. NM_111200.5. [Q3EBC8-1 ]
UniGenei At.43488.

3D structure databases

ProteinModelPortali Q3EBC8.
SMRi Q3EBC8. Positions 11-510, 558-638, 1152-1385.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q3EBC8. 4 interactions.
STRINGi 3702.AT3G03300.1-P.

Proteomic databases

PaxDbi Q3EBC8.
PRIDEi Q3EBC8.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT3G03300.1 ; AT3G03300.1 ; AT3G03300 . [Q3EBC8-1 ]
AT3G03300.3 ; AT3G03300.3 ; AT3G03300 . [Q3EBC8-1 ]
GeneIDi 821300.
KEGGi ath:AT3G03300.

Organism-specific databases

TAIRi AT3G03300.

Phylogenomic databases

eggNOGi COG1111.
HOGENOMi HOG000006099.
InParanoidi Q3EBC8.
KOi K11592.
OMAi HILHASH.
PhylomeDBi Q3EBC8.

Enzyme and pathway databases

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

Gene expression databases

Genevestigatori Q3EBC8.

Family and domain databases

Gene3Di 1.10.1520.10. 2 hits.
3.40.50.300. 2 hits.
InterProi IPR005034. 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 ]
Pfami PF00270. DEAD. 1 hit.
PF03368. Dicer_dimer. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF00636. Ribonuclease_3. 2 hits.
[Graphical view ]
SMARTi SM00487. DEXDc. 1 hit.
SM00358. DSRM. 1 hit.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view ]
SUPFAMi SSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 4 hits.
PROSITEi 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 ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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. 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.

Entry informationi

Entry nameiDCL2_ARATH
AccessioniPrimary (citable) accession number: Q3EBC8
Secondary accession number(s): Q1KL57, Q1KL58, Q9M9P8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 8, 2011
Last sequence update: January 15, 2008
Last modified: September 3, 2014
This is version 81 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi