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Protein

Dicer-like protein 4

Gene

DCL4

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). Functions in the biogenesis of trans-acting small interfering RNAs (ta-siRNAs, derived from the TAS1, TAS2 or TAS3 endogenous transcripts) by cleaving small dsRNAs into 21-24 nucleotide ta-siRNAs. Functions with the dsRNA-binding protein DRB4 in ta-siRNAs processing. Acts in the RDR6/SGS3/DCL4/AGO7 ta-siRNA pathway involved in leaf developmental timing. Plays a role in transitive silencing of transgenes by processing secondary siRNAs. This pathway, which requires DCL2 and RDR6, amplifies silencing by using the target RNA as substrate to generate secondary siRNAs, providing an efficient mechanism for long-distance silencing. Required for the production of the 30-40 nucleotide bacterial-induced long siRNAs (lsiRNA). 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 an important role in antiviral RNA silencing. Involved in the production of viral siRNAs derived from the cucumber mosaic virus (CMV), 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 DCL4 function in RNA silencing. Does not seem to be involved in microRNAs (miRNAs) processing.11 Publications

Cofactori

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1330Magnesium or manganeseBy similarity1
Sitei1418Important for activityBy similarity1
Metal bindingi1422Magnesium or manganeseBy similarity1
Metal bindingi1425Magnesium or manganeseBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi144 – 151ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

  • defense response to virus Source: TAIR
  • DNA-templated transcription, termination Source: TAIR
  • maintenance of DNA methylation Source: TAIR
  • maintenance of shoot apical meristem identity Source: EnsemblPlants
  • polarity specification of adaxial/abaxial axis Source: EnsemblPlants
  • production of lsiRNA involved in RNA interference Source: TAIR
  • production of ta-siRNAs involved in RNA interference Source: TAIR
  • reproductive structure development Source: EnsemblPlants
  • RNA virus induced gene silencing Source: TAIR
  • vegetative phase change Source: TAIR
  • 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, Metal-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Dicer-like protein 4 (EC:3.1.26.-)
Gene namesi
Name:DCL4
Ordered Locus Names:At5g20320
ORF Names:F5O24.210
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G20320.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: GO_Central
  • nucleus Source: TAIR
  • RISC complex Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001804751 – 1702Dicer-like protein 4Add BLAST1702

Proteomic databases

PaxDbiP84634.
PRIDEiP84634.

PTM databases

iPTMnetiP84634.

Expressioni

Gene expression databases

ExpressionAtlasiP84634. baseline and differential.
GenevisibleiP84634. AT.

Interactioni

Subunit structurei

Interacts with DRB4.1 Publication

Protein-protein interaction databases

BioGridi17430. 4 interactors.
IntActiP84634. 2 interactors.
MINTiMINT-6948367.
STRINGi3702.AT5G20320.1.

Structurei

Secondary structure

11702
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi655 – 664Combined sources10
Beta strandi667 – 669Combined sources3
Beta strandi678 – 683Combined sources6
Helixi686 – 688Combined sources3
Beta strandi690 – 695Combined sources6
Beta strandi705 – 708Combined sources4
Helixi713 – 731Combined sources19
Turni735 – 737Combined sources3
Helixi741 – 744Combined sources4
Turni748 – 750Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KOUNMR-A651-752[»]
ProteinModelPortaliP84634.
SMRiP84634.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP84634.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini131 – 307Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST177
Domaini475 – 629Helicase C-terminalPROSITE-ProRule annotationAdd BLAST155
Domaini656 – 748Dicer dsRNA-binding foldPROSITE-ProRule annotationAdd BLAST93
Domaini927 – 1054PAZPROSITE-ProRule annotationAdd BLAST128
Domaini1083 – 1251RNase III 1PROSITE-ProRule annotationAdd BLAST169
Domaini1292 – 1436RNase III 2PROSITE-ProRule annotationAdd BLAST145
Domaini1462 – 1528DRBM 1PROSITE-ProRule annotationAdd BLAST67
Domaini1621 – 1697DRBM 2PROSITE-ProRule annotationAdd BLAST77

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi251 – 254DECH box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi89 – 102Poly-SerAdd BLAST14

Sequence similaritiesi

Belongs to the helicase family. Dicer subfamily.PROSITE-ProRule annotation
Contains 1 Dicer dsRNA-binding fold domain.PROSITE-ProRule annotation
Contains 2 DRBM (double-stranded RNA-binding) domains.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.
HOGENOMiHOG000083706.
InParanoidiP84634.
KOiK11592.
OMAiQSNHPYA.
OrthoDBiEOG0936003I.
PhylomeDBiP84634.

Family and domain databases

CDDicd00593. RIBOc. 2 hits.
Gene3Di1.10.1520.10. 3 hits.
3.30.160.20. 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. 2 hits.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 3 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]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: P84634-1) [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
MRDEVDLSLT IPSKLLGKRD REQKNCEEEK NKNKKAKKQQ KDPILLHTSA
60 70 80 90 100
ATHKFLPPPL TMPYSEIGDD LRSLDFDHAD VSSDLHLTSS SSVSSFSSSS
110 120 130 140 150
SSLFSAAGTD DPSPKMEKDP RKIARRYQVE LCKKATEENV IVYLGTGCGK
160 170 180 190 200
THIAVMLIYE LGHLVLSPKK SVCIFLAPTV ALVEQQAKVI ADSVNFKVAI
210 220 230 240 250
HCGGKRIVKS HSEWEREIAA NEVLVMTPQI LLHNLQHCFI KMECISLLIF
260 270 280 290 300
DECHHAQQQS NHPYAEIMKV FYKSESLQRP RIFGMTASPV VGKGSFQSEN
310 320 330 340 350
LSKSINSLEN LLNAKVYSVE SNVQLDGFVS SPLVKVYYYR SALSDASQST
360 370 380 390 400
IRYENMLEDI KQRCLASLKL LIDTHQTQTL LSMKRLLKRS HDNLIYTLLN
410 420 430 440 450
LGLWGAIQAA KIQLNSDHNV QDEPVGKNPK SKICDTYLSM AAEALSSGVA
460 470 480 490 500
KDENASDLLS LAALKEPLFS RKLVQLIKIL SVFRLEPHMK CIIFVNRIVT
510 520 530 540 550
ARTLSCILNN LELLRSWKSD FLVGLSSGLK SMSRRSMETI LKRFQSKELN
560 570 580 590 600
LLVATKVGEE GLDIQTCCLV IRYDLPETVT SFIQSRGRAR MPQSEYAFLV
610 620 630 640 650
DSGNEKEMDL IENFKVNEDR MNLEITYRSS EETCPRLDEE LYKVHETGAC
660 670 680 690 700
ISGGSSISLL YKYCSRLPHD EFFQPKPEFQ FKPVDEFGGT ICRITLPANA
710 720 730 740 750
PISEIESSLL PSTEAAKKDA CLKAVHELHN LGVLNDFLLP DSKDEIEDEL
760 770 780 790 800
SDDEFDFDNI KGEGCSRGDL YEMRVPVLFK QKWDPSTSCV NLHSYYIMFV
810 820 830 840 850
PHPADRIYKK FGFFMKSPLP VEAETMDIDL HLAHQRSVSV KIFPSGVTEF
860 870 880 890 900
DNDEIRLAEL FQEIALKVLF ERGELIPDFV PLELQDSSRT SKSTFYLLLP
910 920 930 940 950
LCLHDGESVI SVDWVTIRNC LSSPIFKTPS VLVEDIFPPS GSHLKLANGC
960 970 980 990 1000
WNIDDVKNSL VFTTYSKQFY FVADICHGRN GFSPVKESST KSHVESIYKL
1010 1020 1030 1040 1050
YGVELKHPAQ PLLRVKPLCH VRNLLHNRMQ TNLEPQELDE YFIEIPPELS
1060 1070 1080 1090 1100
HLKIKGLSKD IGSSLSLLPS IMHRMENLLV AIELKHVLSA SIPEIAEVSG
1110 1120 1130 1140 1150
HRVLEALTTE KCHERLSLER LEVLGDAFLK FAVSRHLFLH HDSLDEGELT
1160 1170 1180 1190 1200
RRRSNVVNNS NLCRLAIKKN LQVYIRDQAL DPTQFFAFGH PCRVTCDEVA
1210 1220 1230 1240 1250
SKEVHSLNRD LGILESNTGE IRCSKGHHWL YKKTIADVVE ALVGAFLVDS
1260 1270 1280 1290 1300
GFKGAVKFLK WIGVNVDFES LQVQDACIAS RRYLPLTTRN NLETLENQLD
1310 1320 1330 1340 1350
YKFLHKGLLV QAFIHPSYNR HGGGCYQRLE FLGDAVLDYL MTSYFFTVFP
1360 1370 1380 1390 1400
KLKPGQLTDL RSLSVNNEAL ANVAVSFSLK RFLFCESIYL HEVIEDYTNF
1410 1420 1430 1440 1450
LASSPLASGQ SEGPRCPKVL GDLVESCLGA LFLDCGFNLN HVWTMMLSFL
1460 1470 1480 1490 1500
DPVKNLSNLQ ISPIKELIEL CQSYKWDREI SATKKDGAFT VELKVTKNGC
1510 1520 1530 1540 1550
CLTVSATGRN KREGTKKAAQ LMITNLKAHE NITTSHPLED VLKNGIRNEA
1560 1570 1580 1590 1600
KLIGYNEDPI DVVDLVGLDV ENLNILETFG GNSERSSSYV IRRGLPQAPS
1610 1620 1630 1640 1650
KTEDRLPQKA IIKAGGPSSK TAKSLLHETC VANCWKPPHF ECCEEEGPGH
1660 1670 1680 1690 1700
LKSFVYKVIL EVEDAPNMTL ECYGEARATK KGAAEHAAQA AIWCLKHSGF

LC
Length:1,702
Mass (Da):191,279
Last modified:February 8, 2011 - v2
Checksum:i7AA7647A6BA7F24D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ118423 mRNA. Translation: AAZ80387.1.
AF296825 Genomic DNA. No translation available.
CP002688 Genomic DNA. Translation: AED92830.1.
RefSeqiNP_197532.3. NM_122039.5. [P84634-1]
UniGeneiAt.31201.

Genome annotation databases

EnsemblPlantsiAT5G20320.1; AT5G20320.1; AT5G20320. [P84634-1]
GeneIDi832154.
GrameneiAT5G20320.1; AT5G20320.1; AT5G20320.
KEGGiath:AT5G20320.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ118423 mRNA. Translation: AAZ80387.1.
AF296825 Genomic DNA. No translation available.
CP002688 Genomic DNA. Translation: AED92830.1.
RefSeqiNP_197532.3. NM_122039.5. [P84634-1]
UniGeneiAt.31201.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KOUNMR-A651-752[»]
ProteinModelPortaliP84634.
SMRiP84634.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi17430. 4 interactors.
IntActiP84634. 2 interactors.
MINTiMINT-6948367.
STRINGi3702.AT5G20320.1.

PTM databases

iPTMnetiP84634.

Proteomic databases

PaxDbiP84634.
PRIDEiP84634.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G20320.1; AT5G20320.1; AT5G20320. [P84634-1]
GeneIDi832154.
GrameneiAT5G20320.1; AT5G20320.1; AT5G20320.
KEGGiath:AT5G20320.

Organism-specific databases

TAIRiAT5G20320.

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
HOGENOMiHOG000083706.
InParanoidiP84634.
KOiK11592.
OMAiQSNHPYA.
OrthoDBiEOG0936003I.
PhylomeDBiP84634.

Miscellaneous databases

EvolutionaryTraceiP84634.
PROiP84634.

Gene expression databases

ExpressionAtlasiP84634. baseline and differential.
GenevisibleiP84634. AT.

Family and domain databases

CDDicd00593. RIBOc. 2 hits.
Gene3Di1.10.1520.10. 3 hits.
3.30.160.20. 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. 2 hits.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 3 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 nameiDCL4_ARATH
AccessioniPrimary (citable) accession number: P84634
Secondary accession number(s): Q3SA53
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 13, 2005
Last sequence update: February 8, 2011
Last modified: November 30, 2016
This is version 98 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.