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Protein

Endoribonuclease Dicer homolog 2

Gene

At3g03300

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1188Magnesium or manganeseBy similarity1
Sitei1278Important for activityBy similarity1
Metal bindingi1282Magnesium or manganeseBy similarity1
Metal bindingi1285Magnesium or manganeseBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi44 – 51ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

  • maintenance of DNA methylation Source: TAIR
  • production of ta-siRNAs involved in RNA interference Source: TAIR
  • RNA virus induced gene silencing 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

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
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G03300.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004046601 – 1388Endoribonuclease Dicer homolog 2Add BLAST1388

Proteomic databases

PaxDbiQ3EBC8.
PRIDEiQ3EBC8.

PTM databases

iPTMnetiQ3EBC8.

Expressioni

Gene expression databases

GenevisibleiQ3EBC8. AT.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

IntActiQ3EBC8. 4 interactors.
STRINGi3702.AT3G03300.1.

Structurei

3D structure databases

ProteinModelPortaliQ3EBC8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini31 – 210Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST180
Domaini380 – 544Helicase C-terminalPROSITE-ProRule annotationAdd BLAST165
Domaini559 – 645Dicer dsRNA-binding foldPROSITE-ProRule annotationAdd BLAST87
Domaini807 – 935PAZPROSITE-ProRule annotationAdd BLAST129
Domaini962 – 1113RNase III 1PROSITE-ProRule annotationAdd BLAST152
Domaini1149 – 1296RNase III 2PROSITE-ProRule annotationAdd BLAST148
Domaini1315 – 1384DRBMPROSITE-ProRule annotationAdd BLAST70

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi152 – 155DECH box4

Sequence similaritiesi

Belongs to the helicase family. Dicer subfamily.PROSITE-ProRule annotation
Contains 1 Dicer dsRNA-binding fold domain.PROSITE-ProRule annotation
Contains 1 DRBM (double-stranded RNA-binding) domain.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 PAZ domain.PROSITE-ProRule annotation
Contains 2 RNase III domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
HOGENOMiHOG000006099.
InParanoidiQ3EBC8.
KOiK11592.
OMAiNEHITAA.
OrthoDBiEOG0936003I.
PhylomeDBiQ3EBC8.

Family and domain databases

CDDicd00593. RIBOc. 2 hits.
Gene3Di1.10.1520.10. 2 hits.
3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR005034. Dicer_dimerisation_dom.
IPR014720. dsRBD_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. AlignAdd to basket

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

        10         20         30         40         50
MTMDADAMET ETTDQVSASP LHFARSYQVE ALEKAIKQNT IVFLETGSGK
60 70 80 90 100
TLIAIMLLRS YAYLFRKPSP CFCVFLVPQV VLVTQQAEAL KMHTDLKVGM
110 120 130 140 150
YWGDMGVDFW DSSTWKQEVD KYEVLVMTPA ILLDALRHSF LSLSMIKVLI
160 170 180 190 200
VDECHHAGGK HPYACIMREF YHKELNSGTS NVPRIFGMTA SLVKTKGENL
210 220 230 240 250
DSYWKKIHEL ETLMNSKVYT CENESVLAGF VPFSTPSFKY YQHIKIPSPK
260 270 280 290 300
RASLVEKLER LTIKHRLSLG TLDLNSSTVD SVEKRLLRIS STLTYCLDDL
310 320 330 340 350
GILLAQKAAQ SLSASQNDSF LWGELNMFSV ALVKKFCSDA SQEFLAEIPQ
360 370 380 390 400
GLNWSVANIN GNAEAGLLTL KTVCLIETLL GYSSLENIRC IIFVDRVITA
410 420 430 440 450
IVLESLLAEI LPNCNNWKTK YVAGNNSGLQ NQTRKKQNEI VEDFRRGLVN
460 470 480 490 500
IIVATSILEE GLDVQSCNLV IRFDPASNIC SFIQSRGRAR MQNSDYLMMV
510 520 530 540 550
ESGDLLTQSR LMKYLSGGKR MREESLDHSL VPCPPLPDDS DEPLFRVEST
560 570 580 590 600
GATVTLSSSV SLIYHYCSRL PSDEYFKPAP RFDVNKDQGS CTLYLPKSCP
610 620 630 640 650
VKEVKAEANN KVLKQAVCLK ACIQLHKVGA LSDHLVPDMV VAETVSQKLE
660 670 680 690 700
KIQYNTEQPC YFPPELVSQF SAQPETTYHF YLIRMKPNSP RNFHLNDVLL
710 720 730 740 750
GTRVVLEDDI GNTSFRLEDH RGTIAVTLSY VGAFHLTQEE VLFCRRFQIT
760 770 780 790 800
LFRVLLDHSV ENLMEALNGL HLRDGVALDY LLVPSTHSHE TSLIDWEVIR
810 820 830 840 850
SVNLTSHEVL EKHENCSTNG ASRILHTKDG LFCTCVVQNA LVYTPHNGYV
860 870 880 890 900
YCTKGVLNNL NGNSLLTKRN SGDQTYIEYY EERHGIQLNF VDEPLLNGRH
910 920 930 940 950
IFTLHSYLHM AKKKKEKEHD REFVELPPEL CHVILSPISV DMIYSYTFIP
960 970 980 990 1000
SVMQRIESLL IAYNLKKSIP KVNIPTIKVL EAITTKKCED QFHLESLETL
1010 1020 1030 1040 1050
GDSFLKYAVC QQLFQHCHTH HEGLLSTKKD GMISNVMLCQ FGCQQKLQGF
1060 1070 1080 1090 1100
IRDECFEPKG WMVPGQSSAA YSLVNDTLPE SRNIYVASRR NLKRKSVADV
1110 1120 1130 1140 1150
VESLIGAYLS EGGELAALMF MNWVGIKVDF TTTKIQRDSP IQAEKLVNVG
1160 1170 1180 1190 1200
YMESLLNYSF EDKSLLVEAL THGSYMMPEI PRCYQRLEFL GDSVLDYLIT
1210 1220 1230 1240 1250
KHLYDKYPCL SPGLLTDMRS ASVNNECYAL VAVKANLHKH ILYASHHLHK
1260 1270 1280 1290 1300
HISRTVSEFE QSSLQSTFGW ESDISFPKVL GDVIESLAGA IFVDSGYNKE
1310 1320 1330 1340 1350
VVFASIKPLL GCMITPETVK LHPVRELTEL CQKWQFELSK AKDFDSFTVE
1360 1370 1380
VKAKEMSFAH TAKASDKKMA KKLAYKEVLN LLKNSLDY
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 AAF26098 differs from that shown. Reason: Erroneous gene model prediction. The predicted gene At3g03300 has been split into 2 genes: At3g03300 and At3g03305.Curated
The sequence ABF19797 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti511L → S in ABF19797 (PubMed:16638569).Curated1
Sequence conflicti511L → S in ABF19798 (PubMed:16638569).Curated1
Sequence conflicti693F → L in ABF19797 (PubMed:16638569).Curated1
Sequence conflicti693F → L in ABF19798 (PubMed:16638569).Curated1
Sequence conflicti738Q → R in ABF19797 (PubMed:16638569).Curated1
Sequence conflicti738Q → R in ABF19798 (PubMed:16638569).Curated1
Sequence conflicti1130F → L in ABF19797 (PubMed:16638569).Curated1
Sequence conflicti1130F → L in ABF19798 (PubMed:16638569).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0406151 – 83MTMDA…QVVLV → MLLCLLGSSSGSCHSGIGVR IGVVDKGIHQYTDLSFVLQF LHYYTCSFSKFRNFSVTFSI ISAFFLVCF in isoform 2. 1 PublicationAdd BLAST83

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001202869.2. [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.
GrameneiAT3G03300.1; AT3G03300.1; AT3G03300.
AT3G03300.3; AT3G03300.3; AT3G03300.
KEGGiath:AT3G03300.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001202869.2. [Q3EBC8-1]
NP_566199.4. NM_111200.5. [Q3EBC8-1]
UniGeneiAt.43488.

3D structure databases

ProteinModelPortaliQ3EBC8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ3EBC8. 4 interactors.
STRINGi3702.AT3G03300.1.

PTM databases

iPTMnetiQ3EBC8.

Proteomic databases

PaxDbiQ3EBC8.
PRIDEiQ3EBC8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G03300.1; AT3G03300.1; AT3G03300. [Q3EBC8-1]
AT3G03300.3; AT3G03300.3; AT3G03300. [Q3EBC8-1]
GeneIDi821300.
GrameneiAT3G03300.1; AT3G03300.1; AT3G03300.
AT3G03300.3; AT3G03300.3; AT3G03300.
KEGGiath:AT3G03300.

Organism-specific databases

TAIRiAT3G03300.

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
HOGENOMiHOG000006099.
InParanoidiQ3EBC8.
KOiK11592.
OMAiNEHITAA.
OrthoDBiEOG0936003I.
PhylomeDBiQ3EBC8.

Miscellaneous databases

PROiQ3EBC8.

Gene expression databases

GenevisibleiQ3EBC8. AT.

Family and domain databases

CDDicd00593. RIBOc. 2 hits.
Gene3Di1.10.1520.10. 2 hits.
3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR005034. Dicer_dimerisation_dom.
IPR014720. dsRBD_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]
ProtoNetiSearch...

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: November 30, 2016
This is version 100 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.