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Protein

Endoribonuclease Dicer homolog 3

Gene

DCL3

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 repeat-associated small interfering RNAs (ra-siRNAs, derived from heterochromatin and DNA repeats such as transposons) by cleaving small dsRNAs into 24 nucleotide ra-siRNAs. Plays a role in antiviral RNA silencing. Involved in the production of viral siRNAs derived from the cabbage leaf curl virus (CaLCuV) and tobacco rattle virus (TRV). Targeted by the viral silencing suppressor (VSR) protein 2b of the cucumber mosaic virus (CMV) that inactivates DCL3 function in RNA silencing. Acts redundantly with DICER-LIKE 1 (DCL1) to promote flowering via repression of FLOWERING LOCUS C (FLC). Does not seem to be involved in microRNAs (miRNAs) processing.5 Publications

Cofactori

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1234Magnesium or manganeseBy similarity1
Sitei1322Important for activityBy similarity1
Metal bindingi1326Magnesium or manganeseBy similarity1
Metal bindingi1329Magnesium or manganeseBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi64 – 71ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

  • maintenance of DNA methylation Source: TAIR
  • multicellular organism development Source: EnsemblPlants
  • production of miRNAs involved in gene silencing by miRNA Source: EnsemblPlants
  • production of siRNA involved in RNA interference Source: TAIR
  • production of ta-siRNAs involved in RNA interference Source: TAIR
  • RNA virus induced gene silencing Source: TAIR

Keywordsi

Molecular functionEndonuclease, Helicase, Hydrolase, Nuclease, RNA-binding
Biological processPlant defense, RNA-mediated gene silencing
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease Dicer homolog 3 (EC:3.1.26.-)
Alternative name(s):
Dicer-like protein 3
Short name:
AtDCL3
Gene namesi
Name:DCL3
Ordered Locus Names:At3g43920
ORF Names:T15B3.60
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

AraportiAT3G43920.
TAIRilocus:2097139. AT3G43920.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004046611 – 1580Endoribonuclease Dicer homolog 3Add BLAST1580

Proteomic databases

PaxDbiQ9LXW7.
PRIDEiQ9LXW7.

Expressioni

Gene expression databases

ExpressionAtlasiQ9LXW7. baseline and differential.
GenevisibleiQ9LXW7. AT.

Interactioni

Subunit structurei

Interacts with DRB2 and DRB5.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
DRB3Q9LJF52EBI-632737,EBI-10815073

Protein-protein interaction databases

BioGridi8828. 5 interactors.
IntActiQ9LXW7. 3 interactors.
STRINGi3702.AT3G43920.2.

Structurei

3D structure databases

ProteinModelPortaliQ9LXW7.
SMRiQ9LXW7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini51 – 223Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST173
Domaini394 – 562Helicase C-terminalPROSITE-ProRule annotationAdd BLAST169
Domaini821 – 934PAZPROSITE-ProRule annotationAdd BLAST114
Domaini985 – 1157RNase III 1PROSITE-ProRule annotationAdd BLAST173
Domaini1198 – 1340RNase III 2PROSITE-ProRule annotationAdd BLAST143

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi170 – 173DECH box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi622 – 630Poly-Ser9

Sequence similaritiesi

Belongs to the helicase family. Dicer subfamily.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
HOGENOMiHOG000030250.
InParanoidiQ9LXW7.
KOiK11592.
OMAiGPWCADK.
OrthoDBiEOG0936003I.
PhylomeDBiQ9LXW7.

Family and domain databases

CDDicd00079. HELICc. 1 hit.
cd00593. RIBOc. 2 hits.
Gene3Di1.10.1520.10. 2 hits.
InterProiView protein in InterPro
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR003100. PAZ_dom.
IPR036085. PAZ_dom_sf.
IPR000999. RNase_III_dom.
IPR036389. RNase_III_sf.
PfamiView protein in Pfam
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF00636. Ribonuclease_3. 2 hits.
SMARTiView protein in SMART
SM00487. DEXDc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 3 hits.
PROSITEiView protein in PROSITE
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.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9LXW7-1) [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
MHSSLEPEKM EEGGGSNSLK RKFSEIDGDQ NLDSVSSPMM TDSNGSYELK
60 70 80 90 100
VYEVAKNRNI IAVLGTGIDK SEITKRLIKA MGSSDTDKRL IIFLAPTVNL
110 120 130 140 150
VKQQCCEIRA LVNLKVEEYF GAKGVDKWTS QRWDEEFSKH DVLVMTPQIL
160 170 180 190 200
LDVLRSAFLK LEMVCLLIID ECHHTTGNHP YAKLMKEFYH ESTSKPKIFG
210 220 230 240 250
LTASAVIRKG IVSSPSNYAA QVSELERLMD SKIFNPEERE GVEKFATTVK
260 270 280 290 300
EGPILYNPSP SCSLELKEKL ETSHLKFDAS LRRLQELGKD SFLNMDNKFE
310 320 330 340 350
TYQKRLSIDY REILHCLDNL GLICAHLAAE VCLEKISDTK EESETYKECS
360 370 380 390 400
MVCKEFLEDI LSTIGVYLPQ DDKSLVDLQQ NHLSAVISGH VSPKLKELFH
410 420 430 440 450
LLDSFRGDKQ KQCLILVERI ITAKVIERFV KKEASLAYLN VLYLTENNPS
460 470 480 490 500
TNVSAQKMQI EIPDLFQHGK VNLLFITDVV EEGFQVPDCS CMVCFDLPKT
510 520 530 540 550
MCSYSQSQKH AKQSNSKSIM FLERGNPKQR DHLHDLMRRE VLIQDPEAPN
560 570 580 590 600
LKSCPPPVKN GHGVKEIGSM VIPDSNITVS EEAASTQTMS DPPSRNEQLP
610 620 630 640 650
PCKKLRLDNN LLQSNGKEKV ASSKSKSSSS AAGSKKRKEL HGTTCANALS
660 670 680 690 700
GTWGENIDGA TFQAYKFDFC CNISGEVYSS FSLLLESTLA EDVGKVEMDL
710 720 730 740 750
YLVRKLVKAS VSPCGQIRLS QEELVKAKYF QQFFFNGMFG KLFVGSKSQG
760 770 780 790 800
TKREFLLQTD TSSLWHPAFM FLLLPVETND LASSATIDWS AINSCASIVE
810 820 830 840 850
FLKKNSLLDL RDSDGNQCNT SSGQEVLLDD KMEETNLIHF ANASSDKNSL
860 870 880 890 900
EELVVIAIHT GRIYSIVEAV SDSSAMSPFE VDASSGYATY AEYFNKKYGI
910 920 930 940 950
VLAHPNQPLM KLKQSHHAHN LLVDFNEEMV VKTEPKAGNV RKRKPNIHAH
960 970 980 990 1000
LPPELLARID VPRAVLKSIY LLPSVMHRLE SLMLASQLRE EIDCSIDNFS
1010 1020 1030 1040 1050
ISSTSILEAV TTLTCPESFS MERLELLGDS VLKYVASCHL FLKYPDKDEG
1060 1070 1080 1090 1100
QLSRQRQSII SNSNLHRLTT SRKLQGYIRN GAFEPRRWTA PGQFSLFPVP
1110 1120 1130 1140 1150
CKCGIDTREV PLDPKFFTEN MTIKIGKSCD MGHRWVVSKS VSDCAEALIG
1160 1170 1180 1190 1200
AYYVSGGLSA SLHMMKWLGI DVDFDPNLVV EAINRVSLRC YIPKEDELIE
1210 1220 1230 1240 1250
LERKIQHEFS AKFLLKEAIT HSSLRESYSY ERLEFLGDSV LDFLITRHLF
1260 1270 1280 1290 1300
NTYEQTGPGE MTDLRSACVN NENFAQVAVK NNLHTHLQRC ATVLETQIND
1310 1320 1330 1340 1350
YLMSFQKPDE TGRSIPSIQG PKALGDVVES IAGALLIDTR LDLDQVWRVF
1360 1370 1380 1390 1400
EPLLSPLVTP DKLQLPPYRE LNELCDSLGY FFRVKCSNDG VKAQATIQLQ
1410 1420 1430 1440 1450
LDDVLLTGDG SEQTNKLALG KAASHLLTQL EKRNISRKTS LGDNQSSMDV
1460 1470 1480 1490 1500
NLACNHSDRE TLTSETTEIQ SIVIPFIGPI NMKKGGPRGT LHEFCKKHLW
1510 1520 1530 1540 1550
PMPTFDTSEE KSRTPFEFID GGEKRTSFSS FTSTITLRIP NREAVMYAGE
1560 1570 1580
ARPDKKSSFD SAVVELLYEL ERRKIVIIQK
Note: Derived from EST data. No experimental confirmation available.
Length:1,580
Mass (Da):177,425
Last modified:February 8, 2011 - v2
Checksum:iEA71D47BF3C29FA5
GO
Isoform 2 (identifier: Q9LXW7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     101-103: Missing.
     186-231: Missing.

Show »
Length:1,531
Mass (Da):172,014
Checksum:i43EC275D4EA33BD7
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_040616101 – 103Missing in isoform 2. 1 Publication3
Alternative sequenceiVSP_040617186 – 231Missing in isoform 2. 1 PublicationAdd BLAST46

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ479972 mRNA. Translation: ABF19799.1.
AL163975 Genomic DNA. Translation: CAB88120.1.
CP002686 Genomic DNA. Translation: AEE77842.1.
CP002686 Genomic DNA. Translation: AEE77843.1.
PIRiT48946.
RefSeqiNP_001154662.2. NM_001161190.2. [Q9LXW7-1]
NP_189978.1. NM_114260.1. [Q9LXW7-2]
UniGeneiAt.36217.
At.50849.

Genome annotation databases

EnsemblPlantsiAT3G43920.1; AT3G43920.1; AT3G43920. [Q9LXW7-2]
AT3G43920.2; AT3G43920.2; AT3G43920. [Q9LXW7-1]
GeneIDi823508.
GrameneiAT3G43920.1; AT3G43920.1; AT3G43920.
AT3G43920.2; AT3G43920.2; AT3G43920.
KEGGiath:AT3G43920.

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiDCL3_ARATH
AccessioniPrimary (citable) accession number: Q9LXW7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 8, 2011
Last sequence update: February 8, 2011
Last modified: October 25, 2017
This is version 114 of the entry and version 2 of the sequence. See 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