Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9SP32 (DCL1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 117. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:DCL1
Synonyms:ASU1, CAF SIN1, SUS1
Ordered Locus Names:At1g01040
ORF Names:T25K16.4
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length1909 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11 Ref.13

Cofactor

Magnesium or manganese By similarity. HAMAP-Rule MF_00104

Subunit structure

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. Ref.6 Ref.7 Ref.12

Subcellular location

Nucleus. Note: Localizes to nuclear dicing body (also named D body), a nuclear body distributed throughout the nucleoplasm and involved in miRNA processing. Ref.6 Ref.8

Tissue specificity

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. Ref.1 Ref.2

Developmental stage

Detected in the embryo, but not in the suspensor, up to the globular stage. Ref.2

Disruption phenotype

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. Ref.1 Ref.2

Miscellaneous

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

Sequence similarities

Belongs to the helicase family. Dicer subfamily.

Contains 1 Dicer dsRNA-binding fold domain.

Contains 2 DRBM (double-stranded RNA-binding) domains.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Contains 1 PAZ domain.

Contains 2 RNase III domains.

Sequence caution

The sequence AAF26461.1 differs from that shown. Reason: Erroneous gene model prediction.

Binary interactions

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q9SP32-1)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 19091909Endoribonuclease Dicer homolog 1 HAMAP-Rule MF_00104
PRO_0000180472

Regions

Domain256 – 433178Helicase ATP-binding
Domain651 – 812162Helicase C-terminal
Domain840 – 93596Dicer dsRNA-binding fold
Domain1180 – 1318139PAZ
Domain1342 – 1518177RNase III 1
Domain1559 – 1707149RNase III 2
Domain1733 – 179664DRBM 1
Domain1831 – 190676DRBM 2
Nucleotide binding269 – 2768ATP Potential
Motif378 – 3814DECH box HAMAP-Rule MF_00104

Sites

Metal binding15971Magnesium or manganese By similarity
Metal binding16931Magnesium or manganese By similarity
Metal binding16961Magnesium or manganese By similarity
Site16891Important for activity By similarity

Experimental info

Mutagenesis3951E → K in dcl1-13; early-flowering and decreased number of leaves. Suppresses hyl1 mutant phenotype. Ref.14
Mutagenesis4151P → S in sin1-1; impaired reproductive development. Ref.2
Mutagenesis4311I → K in sin1-2; impaired reproductive development. Ref.2
Mutagenesis1837 – 18437NDICLRK → IAEIDPG in caf-1; converts the floral meristem to an indeterminate state. Ref.1
Mutagenesis1844 – 190966Missing in caf-1; converts the floral meristem to an indeterminate state. Ref.1
Sequence conflict1481S → F in AAF03534. Ref.1
Sequence conflict9881Y → H in AAF03534. Ref.1

Secondary structure

............. 1909
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified September 19, 2003. Version 2.
Checksum: EAA944F0C0C81D4C

FASTA1,909213,574
        10         20         30         40         50         60 
MVMEDEPREA TIKPSYWLDA CEDISCDLID DLVSEFDPSS VAVNESTDEN GVINDFFGGI 

        70         80         90        100        110        120 
DHILDSIKNG GGLPNNGVSD TNSQINEVTV TPQVIAKETV KENGLQKNGG KRDEFSKEEG 

       130        140        150        160        170        180 
DKDRKRARVC SYQSERSNLS GRGHVNNSRE GDRFMNRKRT RNWDEAGNNK KKRECNNYRR 

       190        200        210        220        230        240 
DGRDREVRGY WERDKVGSNE LVYRSGTWEA DHERDVKKVS GGNRECDVKA EENKSKPEER 

       250        260        270        280        290        300 
KEKVVEEQAR RYQLDVLEQA KAKNTIAFLE TGAGKTLIAI LLIKSVHKDL MSQNRKMLSV 

       310        320        330        340        350        360 
FLVPKVPLVY QQAEVIRNQT CFQVGHYCGE MGQDFWDSRR WQREFESKQV LVMTAQILLN 

       370        380        390        400        410        420 
ILRHSIIRME TIDLLILDEC HHAVKKHPYS LVMSEFYHTT PKDKRPAIFG MTASPVNLKG 

       430        440        450        460        470        480 
VSSQVDCAIK IRNLETKLDS TVCTIKDRKE LEKHVPMPSE IVVEYDKAAT MWSLHETIKQ 

       490        500        510        520        530        540 
MIAAVEEAAQ ASSRKSKWQF MGARDAGAKD ELRQVYGVSE RTESDGAANL IHKLRAINYT 

       550        560        570        580        590        600 
LAELGQWCAY KVGQSFLSAL QSDERVNFQV DVKFQESYLS EVVSLLQCEL LEGAAAEKVA 

       610        620        630        640        650        660 
AEVGKPENGN AHDEMEEGEL PDDPVVSGGE HVDEVIGAAV ADGKVTPKVQ SLIKLLLKYQ 

       670        680        690        700        710        720 
HTADFRAIVF VERVVAALVL PKVFAELPSL SFIRCASMIG HNNSQEMKSS QMQDTISKFR 

       730        740        750        760        770        780 
DGHVTLLVAT SVAEEGLDIR QCNVVMRFDL AKTVLAYIQS RGRARKPGSD YILMVERGNV 

       790        800        810        820        830        840 
SHAAFLRNAR NSEETLRKEA IERTDLSHLK DTSRLISIDA VPGTVYKVEA TGAMVSLNSA 

       850        860        870        880        890        900 
VGLVHFYCSQ LPGDRYAILR PEFSMEKHEK PGGHTEYSCR LQLPCNAPFE ILEGPVCSSM 

       910        920        930        940        950        960 
RLAQQAVCLA ACKKLHEMGA FTDMLLPDKG SGQDAEKADQ DDEGEPVPGT ARHREFYPEG 

       970        980        990       1000       1010       1020 
VADVLKGEWV SSGKEVCESS KLFHLYMYNV RCVDFGSSKD PFLSEVSEFA ILFGNELDAE 

      1030       1040       1050       1060       1070       1080 
VLSMSMDLYV ARAMITKASL AFKGSLDITE NQLSSLKKFH VRLMSIVLDV DVEPSTTPWD 

      1090       1100       1110       1120       1130       1140 
PAKAYLFVPV TDNTSMEPIK GINWELVEKI TKTTAWDNPL QRARPDVYLG TNERTLGGDR 

      1150       1160       1170       1180       1190       1200 
REYGFGKLRH NIVFGQKSHP TYGIRGAVAS FDVVRASGLL PVRDAFEKEV EEDLSKGKLM 

      1210       1220       1230       1240       1250       1260 
MADGCMVAED LIGKIVTAAH SGKRFYVDSI CYDMSAETSF PRKEGYLGPL EYNTYADYYK 

      1270       1280       1290       1300       1310       1320 
QKYGVDLNCK QQPLIKGRGV SYCKNLLSPR FEQSGESETV LDKTYYVFLP PELCVVHPLS 

      1330       1340       1350       1360       1370       1380 
GSLIRGAQRL PSIMRRVESM LLAVQLKNLI SYPIPTSKIL EALTAASCQE TFCYERAELL 

      1390       1400       1410       1420       1430       1440 
GDAYLKWVVS RFLFLKYPQK HEGQLTRMRQ QMVSNMVLYQ FALVKGLQSY IQADRFAPSR 

      1450       1460       1470       1480       1490       1500 
WSAPGVPPVF DEDTKDGGSS FFDEEQKPVS EENSDVFEDG EMEDGELEGD LSSYRVLSSK 

      1510       1520       1530       1540       1550       1560 
TLADVVEALI GVYYVEGGKI AANHLMKWIG IHVEDDPDEV DGTLKNVNVP ESVLKSIDFV 

      1570       1580       1590       1600       1610       1620 
GLERALKYEF KEKGLLVEAI THASRPSSGV SCYQRLEFVG DAVLDHLITR HLFFTYTSLP 

      1630       1640       1650       1660       1670       1680 
PGRLTDLRAA AVNNENFARV AVKHKLHLYL RHGSSALEKQ IREFVKEVQT ESSKPGFNSF 

      1690       1700       1710       1720       1730       1740 
GLGDCKAPKV LGDIVESIAG AIFLDSGKDT TAAWKVFQPL LQPMVTPETL PMHPVRELQE 

      1750       1760       1770       1780       1790       1800 
RCQQQAEGLE YKASRSGNTA TVEVFIDGVQ VGVAQNPQKK MAQKLAARNA LAALKEKEIA 

      1810       1820       1830       1840       1850       1860 
ESKEKHINNG NAGEDQGENE NGNKKNGHQP FTRQTLNDIC LRKNWPMPSY RCVKEGGPAH 

      1870       1880       1890       1900 
AKRFTFGVRV NTSDRGWTDE CIGEPMPSVK KAKDSAAVLL LELLNKTFS 

« Hide

References

« Hide 'large scale' references
[1]"Disruption of an RNA helicase/RNase III gene in Arabidopsis causes unregulated cell division in floral meristems."
Jacobsen S.E., Running M.P., Meyerowitz E.M.
Development 126:5231-5243(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DISRUPTION PHENOTYPE, MUTAGENESIS OF 1837-ASN--LYS-1843 AND 1844-ASN--SER-1909.
Strain: cv. Wassilewskija.
[2]"SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis."
Golden T.A., Schauer S.E., Lang J.D., Pien S., Mushegian A.R., Grossniklaus U., Meinke D.W., Ray A.
Plant Physiol. 130:808-822(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, MUTAGENESIS OF PRO-415 AND ILE-431.
Strain: cv. Landsberg erecta.
[3]"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. expand/collapse author list , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[4]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[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]"Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana."
Hiraguri A., Itoh R., Kondo N., Nomura Y., Aizawa D., Murai Y., Koiwa H., Seki M., Shinozaki K., Fukuhara T.
Plant Mol. Biol. 57:173-188(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH DRB1; DRB2 AND DRB5.
[7]"The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis."
Kurihara Y., Takashi Y., Watanabe Y.
RNA 12:206-212(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH DRB1.
[8]"Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants."
Fang Y., Spector D.L.
Curr. Biol. 17:818-823(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[9]"A novel class of bacteria-induced small RNAs in Arabidopsis."
Katiyar-Agarwal S., Gao S., Vivian-Smith A., Jin H.
Genes Dev. 21:3123-3134(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[10]"DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana."
Schmitz R.J., Hong L., Fitzpatrick K.E., Amasino R.M.
Genetics 176:1359-1362(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[11]"The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1."
Dong Z., Han M.-H., Fedoroff N.
Proc. Natl. Acad. Sci. U.S.A. 105:9970-9975(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[12]"The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis."
Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker J.C., Chen X.
Proc. Natl. Acad. Sci. U.S.A. 105:10073-10078(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH DDL.
[13]"Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1."
Qu F., Ye X., Morris T.J.
Proc. Natl. Acad. Sci. U.S.A. 105:14732-14737(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[14]"A dominant mutation in DCL1 suppresses the hyl1 mutant phenotype by promoting the processing of miRNA."
Tagami Y., Motose H., Watanabe Y.
RNA 15:450-458(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLU-395.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_171612.1. NM_099986.3.
UniGeneAt.22088.
At.57123.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2LRSNMR-A1837-1907[»]
ProteinModelPortalQ9SP32.
SMRQ9SP32. Positions 246-803, 835-939, 1208-1440, 1559-1907.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid24809. 8 interactions.
DIPDIP-33454N.
IntActQ9SP32. 5 interactions.

Proteomic databases

PaxDbQ9SP32.
PRIDEQ9SP32.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G01040.1; AT1G01040.1; AT1G01040. [Q9SP32-1]
GeneID839574.
KEGGath:AT1G01040.

Organism-specific databases

TAIRAT1G01040.

Phylogenomic databases

eggNOGCOG1111.
HOGENOMHOG000239675.
InParanoidQ9SP32.
KOK11592.
PhylomeDBQ9SP32.
ProtClustDBCLSN2682824.

Enzyme and pathway databases

BioCycARA:AT1G01040-MONOMER.
ARA:GQT-1487-MONOMER.

Gene expression databases

GenevestigatorQ9SP32.

Family and domain databases

Gene3D1.10.1520.10. 3 hits.
3.30.160.20. 2 hits.
3.40.50.300. 2 hits.
HAMAPMF_00104. RNase_III.
InterProIPR005034. Dicer_dimerisation_dom.
IPR014720. dsRNA-bd_dom.
IPR006935. Helicase/UvrB_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR003100. PAZ_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PfamPF03368. 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]
SMARTSM00487. DEXDc. 1 hit.
SM00358. DSRM. 2 hits.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]
SUPFAMSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF69065. SSF69065. 4 hits.
PROSITEPS51327. 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]
ProtoNetSearch...

Entry information

Entry nameDCL1_ARATH
AccessionPrimary (citable) accession number: Q9SP32
Secondary accession number(s): Q9FDY6, Q9MAN0
Entry history
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: September 19, 2003
Last modified: April 16, 2014
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names