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Protein

Endoribonuclease Dicer homolog 1

Gene

DCL1

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 microRNAs (miRNAs) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Functions with DRB1/HYL1 and SERRATE proteins for accurate pri-miRNAs to miRNAs processing. Indirectly involved in the production of trans-acting small interfering RNAs (ta-siRNAs) derived from the TAS1, TAS2 or TAS3 endogenous transcripts by participating in the production of their initiating miRNAs. Involved in the processing of natural siRNAs (nat-siRNAs, derived from cis-natural antisense transcripts) by cleaving 24 nucleotide nat-siRNAs into 21 nucleotide nat-siRNAs. Can produce RDR6-dependent endogenous ta-siRNAs derived from TAS1 and TAS2. Required for the production of 30-40 nucleotide bacterial-induced long siRNAs (lsiRNA). Acts redundantly with DICER-LIKE 3 (DCL3) to promote flowering via repression of FLOWERING LOCUS C (FLC). Represses antiviral RNA silencing through negative regulation of the expression of DCL4 and DCL3.7 Publications

Cofactori

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1597Magnesium or manganeseBy similarity1
Sitei1689Important for activityBy similarity1
Metal bindingi1693Magnesium or manganeseBy similarity1
Metal bindingi1696Magnesium or manganeseBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi269 – 276ATPSequence analysis8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Helicase, Hydrolase, Nuclease

Keywords - Biological processi

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 1 (EC:3.1.26.-)
Alternative name(s):
Dicer-like protein 1
Short name:
AtDCL1
Protein ABNORMAL SUSPENSOR 1
Protein CARPEL FACTORY
Protein SHORT INTEGUMENTS 1
Protein SUSPENSOR 1
Gene namesi
Name:DCL1
Synonyms:ASU1, CAF SIN1, SUS1
Ordered Locus Names:At1g01040
ORF Names:T25K16.4
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G01040.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Embryonic lethality in sus-1 mutant. Weaker mutant (caf-1) also exists. Mutant caf-1 produces extra whorls of stamens, indefinite number of carpels and show an absence of axillary inflorescence meristems and abnormally shaped leaves and floral organs.2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi395E → K in dcl1-13; early-flowering and decreased number of leaves. Suppresses hyl1 mutant phenotype. 1 Publication1
Mutagenesisi415P → S in sin1-1; impaired reproductive development. 1 Publication1
Mutagenesisi431I → K in sin1-2; impaired reproductive development. 1 Publication1
Mutagenesisi1837 – 1843NDICLRK → IAEIDPG in caf-1; converts the floral meristem to an indeterminate state. 1 Publication7
Mutagenesisi1844 – 1909Missing in caf-1; converts the floral meristem to an indeterminate state. 1 PublicationAdd BLAST66

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001804721 – 1909Endoribonuclease Dicer homolog 1Add BLAST1909

Proteomic databases

PaxDbiQ9SP32.
PRIDEiQ9SP32.

Expressioni

Tissue specificityi

Highly expressed in flowers and seeds and detected in leaves and stems. Found in ovule integuments, inflorescence and floral meristems, stigma of flowers until just before pollination, vasculature of the funiculus, and embryo.2 Publications

Developmental stagei

Detected in the embryo, but not in the suspensor, up to the globular stage.1 Publication

Gene expression databases

ExpressionAtlasiQ9SP32. baseline and differential.
GenevisibleiQ9SP32. AT.

Interactioni

Subunit structurei

Interacts (via N-terminus) with DDL. Interacts (via DRBM domains) with DRB1, DRB2 and DRB5. May interact with AGO1 or AGO10 through their common PAZ domains (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
DDLQ8W4D82EBI-632627,EBI-2015534
DRB1O044923EBI-632627,EBI-632620

Protein-protein interaction databases

BioGridi24809. 10 interactors.
DIPiDIP-33454N.
IntActiQ9SP32. 5 interactors.
STRINGi3702.AT1G01040.2.

Structurei

Secondary structure

11909
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1838 – 1842Combined sources5
Beta strandi1849 – 1854Combined sources6
Beta strandi1864 – 1869Combined sources6
Turni1873 – 1875Combined sources3
Beta strandi1886 – 1888Combined sources3
Helixi1889 – 1903Combined sources15
Helixi1904 – 1906Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LRSNMR-A1837-1907[»]
ProteinModelPortaliQ9SP32.
SMRiQ9SP32.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini256 – 433Helicase ATP-bindingAdd BLAST178
Domaini651 – 812Helicase C-terminalAdd BLAST162
Domaini840 – 935Dicer dsRNA-binding foldAdd BLAST96
Domaini1180 – 1318PAZAdd BLAST139
Domaini1342 – 1518RNase III 1Add BLAST177
Domaini1559 – 1707RNase III 2Add BLAST149
Domaini1733 – 1796DRBM 1Add BLAST64
Domaini1831 – 1906DRBM 2Add BLAST76

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi378 – 381DECH box4

Sequence similaritiesi

Belongs to the helicase family. Dicer subfamily.Curated
Contains 1 helicase ATP-binding domain.Curated
Contains 1 helicase C-terminal domain.Curated
Contains 1 PAZ domain.Curated
Contains 2 RNase III domains.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
HOGENOMiHOG000239675.
InParanoidiQ9SP32.
KOiK11592.
PhylomeDBiQ9SP32.

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.
HAMAPiMF_00104. RNase_III. 1 hit.
InterProiIPR005034. Dicer_dimerisation_dom.
IPR014720. dsRBD_dom.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR003100. PAZ_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF03368. Dicer_dimer. 1 hit.
PF00035. dsrm. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF04851. ResIII. 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]
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 4 hits.
PROSITEiPS51327. DICER_DSRBF. 1 hit.
PS50137. DS_RBD. 2 hits.
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: Q9SP32-1) [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
MVMEDEPREA TIKPSYWLDA CEDISCDLID DLVSEFDPSS VAVNESTDEN
60 70 80 90 100
GVINDFFGGI DHILDSIKNG GGLPNNGVSD TNSQINEVTV TPQVIAKETV
110 120 130 140 150
KENGLQKNGG KRDEFSKEEG DKDRKRARVC SYQSERSNLS GRGHVNNSRE
160 170 180 190 200
GDRFMNRKRT RNWDEAGNNK KKRECNNYRR DGRDREVRGY WERDKVGSNE
210 220 230 240 250
LVYRSGTWEA DHERDVKKVS GGNRECDVKA EENKSKPEER KEKVVEEQAR
260 270 280 290 300
RYQLDVLEQA KAKNTIAFLE TGAGKTLIAI LLIKSVHKDL MSQNRKMLSV
310 320 330 340 350
FLVPKVPLVY QQAEVIRNQT CFQVGHYCGE MGQDFWDSRR WQREFESKQV
360 370 380 390 400
LVMTAQILLN ILRHSIIRME TIDLLILDEC HHAVKKHPYS LVMSEFYHTT
410 420 430 440 450
PKDKRPAIFG MTASPVNLKG VSSQVDCAIK IRNLETKLDS TVCTIKDRKE
460 470 480 490 500
LEKHVPMPSE IVVEYDKAAT MWSLHETIKQ MIAAVEEAAQ ASSRKSKWQF
510 520 530 540 550
MGARDAGAKD ELRQVYGVSE RTESDGAANL IHKLRAINYT LAELGQWCAY
560 570 580 590 600
KVGQSFLSAL QSDERVNFQV DVKFQESYLS EVVSLLQCEL LEGAAAEKVA
610 620 630 640 650
AEVGKPENGN AHDEMEEGEL PDDPVVSGGE HVDEVIGAAV ADGKVTPKVQ
660 670 680 690 700
SLIKLLLKYQ HTADFRAIVF VERVVAALVL PKVFAELPSL SFIRCASMIG
710 720 730 740 750
HNNSQEMKSS QMQDTISKFR DGHVTLLVAT SVAEEGLDIR QCNVVMRFDL
760 770 780 790 800
AKTVLAYIQS RGRARKPGSD YILMVERGNV SHAAFLRNAR NSEETLRKEA
810 820 830 840 850
IERTDLSHLK DTSRLISIDA VPGTVYKVEA TGAMVSLNSA VGLVHFYCSQ
860 870 880 890 900
LPGDRYAILR PEFSMEKHEK PGGHTEYSCR LQLPCNAPFE ILEGPVCSSM
910 920 930 940 950
RLAQQAVCLA ACKKLHEMGA FTDMLLPDKG SGQDAEKADQ DDEGEPVPGT
960 970 980 990 1000
ARHREFYPEG VADVLKGEWV SSGKEVCESS KLFHLYMYNV RCVDFGSSKD
1010 1020 1030 1040 1050
PFLSEVSEFA ILFGNELDAE VLSMSMDLYV ARAMITKASL AFKGSLDITE
1060 1070 1080 1090 1100
NQLSSLKKFH VRLMSIVLDV DVEPSTTPWD PAKAYLFVPV TDNTSMEPIK
1110 1120 1130 1140 1150
GINWELVEKI TKTTAWDNPL QRARPDVYLG TNERTLGGDR REYGFGKLRH
1160 1170 1180 1190 1200
NIVFGQKSHP TYGIRGAVAS FDVVRASGLL PVRDAFEKEV EEDLSKGKLM
1210 1220 1230 1240 1250
MADGCMVAED LIGKIVTAAH SGKRFYVDSI CYDMSAETSF PRKEGYLGPL
1260 1270 1280 1290 1300
EYNTYADYYK QKYGVDLNCK QQPLIKGRGV SYCKNLLSPR FEQSGESETV
1310 1320 1330 1340 1350
LDKTYYVFLP PELCVVHPLS GSLIRGAQRL PSIMRRVESM LLAVQLKNLI
1360 1370 1380 1390 1400
SYPIPTSKIL EALTAASCQE TFCYERAELL GDAYLKWVVS RFLFLKYPQK
1410 1420 1430 1440 1450
HEGQLTRMRQ QMVSNMVLYQ FALVKGLQSY IQADRFAPSR WSAPGVPPVF
1460 1470 1480 1490 1500
DEDTKDGGSS FFDEEQKPVS EENSDVFEDG EMEDGELEGD LSSYRVLSSK
1510 1520 1530 1540 1550
TLADVVEALI GVYYVEGGKI AANHLMKWIG IHVEDDPDEV DGTLKNVNVP
1560 1570 1580 1590 1600
ESVLKSIDFV GLERALKYEF KEKGLLVEAI THASRPSSGV SCYQRLEFVG
1610 1620 1630 1640 1650
DAVLDHLITR HLFFTYTSLP PGRLTDLRAA AVNNENFARV AVKHKLHLYL
1660 1670 1680 1690 1700
RHGSSALEKQ IREFVKEVQT ESSKPGFNSF GLGDCKAPKV LGDIVESIAG
1710 1720 1730 1740 1750
AIFLDSGKDT TAAWKVFQPL LQPMVTPETL PMHPVRELQE RCQQQAEGLE
1760 1770 1780 1790 1800
YKASRSGNTA TVEVFIDGVQ VGVAQNPQKK MAQKLAARNA LAALKEKEIA
1810 1820 1830 1840 1850
ESKEKHINNG NAGEDQGENE NGNKKNGHQP FTRQTLNDIC LRKNWPMPSY
1860 1870 1880 1890 1900
RCVKEGGPAH AKRFTFGVRV NTSDRGWTDE CIGEPMPSVK KAKDSAAVLL

LELLNKTFS
Length:1,909
Mass (Da):213,574
Last modified:September 19, 2003 - v2
Checksum:iEAA944F0C0C81D4C
GO

Sequence cautioni

The sequence AAF26461 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti148S → F in AAF03534 (PubMed:10556049).Curated1
Sequence conflicti988Y → H in AAF03534 (PubMed:10556049).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF187317 mRNA. Translation: AAF03534.1.
AF292940 mRNA. Translation: AAG38019.1.
AF292941 Genomic DNA. Translation: AAG38020.1.
AC007323 Genomic DNA. Translation: AAF26461.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE27220.1.
RefSeqiNP_171612.1. NM_099986.4. [Q9SP32-1]
UniGeneiAt.22088.
At.57123.

Genome annotation databases

EnsemblPlantsiAT1G01040.1; AT1G01040.1; AT1G01040. [Q9SP32-1]
GeneIDi839574.
GrameneiAT1G01040.1; AT1G01040.1; AT1G01040.
KEGGiath:AT1G01040.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF187317 mRNA. Translation: AAF03534.1.
AF292940 mRNA. Translation: AAG38019.1.
AF292941 Genomic DNA. Translation: AAG38020.1.
AC007323 Genomic DNA. Translation: AAF26461.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE27220.1.
RefSeqiNP_171612.1. NM_099986.4. [Q9SP32-1]
UniGeneiAt.22088.
At.57123.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LRSNMR-A1837-1907[»]
ProteinModelPortaliQ9SP32.
SMRiQ9SP32.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi24809. 10 interactors.
DIPiDIP-33454N.
IntActiQ9SP32. 5 interactors.
STRINGi3702.AT1G01040.2.

Proteomic databases

PaxDbiQ9SP32.
PRIDEiQ9SP32.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G01040.1; AT1G01040.1; AT1G01040. [Q9SP32-1]
GeneIDi839574.
GrameneiAT1G01040.1; AT1G01040.1; AT1G01040.
KEGGiath:AT1G01040.

Organism-specific databases

TAIRiAT1G01040.

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
HOGENOMiHOG000239675.
InParanoidiQ9SP32.
KOiK11592.
PhylomeDBiQ9SP32.

Miscellaneous databases

PROiQ9SP32.

Gene expression databases

ExpressionAtlasiQ9SP32. baseline and differential.
GenevisibleiQ9SP32. 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.
HAMAPiMF_00104. RNase_III. 1 hit.
InterProiIPR005034. Dicer_dimerisation_dom.
IPR014720. dsRBD_dom.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR003100. PAZ_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF03368. Dicer_dimer. 1 hit.
PF00035. dsrm. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF04851. ResIII. 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]
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 4 hits.
PROSITEiPS51327. DICER_DSRBF. 1 hit.
PS50137. DS_RBD. 2 hits.
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 nameiDCL1_ARATH
AccessioniPrimary (citable) accession number: Q9SP32
Secondary accession number(s): Q9FDY6, Q9MAN0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: September 19, 2003
Last modified: November 30, 2016
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Expression in the early embryo is from the maternally contributed genome.

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.