ID DCL1_ORYSJ Reviewed; 1883 AA.
AC Q8LMR2; A3ADL0;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 24-JAN-2024, entry version 150.
DE RecName: Full=Endoribonuclease Dicer homolog 1;
DE AltName: Full=Dicer-like protein 1;
DE Short=OsDCL1;
DE EC=3.1.26.-;
GN Name=DCL1; OrderedLocusNames=Os03g0121800, LOC_Os03g02970;
GN ORFNames=OJ1705B08.11, OsJ_09217;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16126864; DOI=10.1104/pp.105.063420;
RA Liu B., Li P., Li X., Liu C., Cao S., Chu C., Cao X.;
RT "Loss of function of OsDCL1 affects microRNA accumulation and causes
RT developmental defects in rice.";
RL Plant Physiol. 139:296-305(2005).
RN [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=18826656; DOI=10.1186/1471-2164-9-451;
RA Kapoor M., Arora R., Lama T., Nijhawan A., Khurana J.P., Tyagi A.K.,
RA Kapoor S.;
RT "Genome-wide identification, organization and phylogenetic analysis of
RT dicer-like, argonaute and RNA-dependent RNA polymerase gene families and
RT their expression analysis during reproductive development and stress in
RT rice.";
RL BMC Genomics 9:451-451(2008).
RN [8]
RP FUNCTION.
RX PubMed=18353984; DOI=10.1073/pnas.0708743105;
RA Lu C., Jeong D.-H., Kulkarni K., Pillay M., Nobuta K., German R.,
RA Thatcher S.R., Maher C., Zhang L., Ware D., Liu B., Cao X., Meyers B.C.,
RA Green P.J.;
RT "Genome-wide analysis for discovery of rice microRNAs reveals natural
RT antisense microRNAs (nat-miRNAs).";
RL Proc. Natl. Acad. Sci. U.S.A. 105:4951-4956(2008).
CC -!- FUNCTION: Involved in the RNA silencing pathway. Cleaves double-
CC stranded RNA to produce microRNAs (miRNAs) of 21-24 nucleotides which
CC target the selective destruction of complementary RNAs. Regulates by
CC this way the development of the plant. May not be involved in small
CC interfering RNAs (siRNAs) production. {ECO:0000269|PubMed:16126864,
CC ECO:0000269|PubMed:18353984}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC -!- SUBUNIT: May interact with ARGONAUTE1 or PINHEAD through their common
CC PAZ domains. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Severe dwarfism and dark green color. Seedling
CC viability compromised. {ECO:0000269|PubMed:16126864}.
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00657}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF10710.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC105363; AAM52322.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF93701.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF10710.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000140; EAZ25399.1; -; Genomic_DNA.
DR AlphaFoldDB; Q8LMR2; -.
DR SMR; Q8LMR2; -.
DR STRING; 39947.Q8LMR2; -.
DR PaxDb; 39947-Q8LMR2; -.
DR EnsemblPlants; Os03t0121800-01; Os03t0121800-01; Os03g0121800.
DR Gramene; Os03t0121800-01; Os03t0121800-01; Os03g0121800.
DR eggNOG; KOG0701; Eukaryota.
DR HOGENOM; CLU_805080_0_0_1; -.
DR InParanoid; Q8LMR2; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004525; F:ribonuclease III activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0035196; P:miRNA processing; IMP:UniProtKB.
DR GO; GO:0030422; P:siRNA processing; IBA:GO_Central.
DR CDD; cd18034; DEXHc_dicer; 1.
DR CDD; cd19869; DSRM_DCL_plant; 1.
DR CDD; cd02844; PAZ_CAF_like; 1.
DR CDD; cd00593; RIBOc; 2.
DR CDD; cd18802; SF2_C_dicer; 1.
DR Gene3D; 3.30.160.20; -; 2.
DR Gene3D; 3.30.160.380; Dicer dimerisation domain; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 3.
DR Gene3D; 2.170.260.10; paz domain; 1.
DR Gene3D; 1.10.1520.10; Ribonuclease III domain; 2.
DR InterPro; IPR038248; Dicer_dimer_sf.
DR InterPro; IPR005034; Dicer_dimerisation_dom.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR003100; PAZ_dom.
DR InterPro; IPR036085; PAZ_dom_sf.
DR InterPro; IPR000999; RNase_III_dom.
DR InterPro; IPR036389; RNase_III_sf.
DR PANTHER; PTHR14950; DICER-RELATED; 1.
DR PANTHER; PTHR14950:SF37; ENDORIBONUCLEASE DICER; 1.
DR Pfam; PF03368; Dicer_dimer; 1.
DR Pfam; PF14709; DND1_DSRM; 1.
DR Pfam; PF00035; dsrm; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF02170; PAZ; 1.
DR Pfam; PF00636; Ribonuclease_3; 2.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00358; DSRM; 2.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00949; PAZ; 1.
DR SMART; SM00535; RIBOc; 2.
DR SUPFAM; SSF54768; dsRNA-binding domain-like; 2.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR SUPFAM; SSF101690; PAZ domain; 1.
DR SUPFAM; SSF69065; RNase III domain-like; 2.
DR PROSITE; PS51327; DICER_DSRBF; 1.
DR PROSITE; PS50137; DS_RBD; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS50821; PAZ; 1.
DR PROSITE; PS00517; RNASE_3_1; 1.
DR PROSITE; PS50142; RNASE_3_2; 2.
PE 3: Inferred from homology;
KW ATP-binding; Endonuclease; Helicase; Hydrolase; Magnesium; Manganese;
KW Metal-binding; Nuclease; Nucleotide-binding; Nucleus; Reference proteome;
KW Repeat; RNA-binding; RNA-mediated gene silencing.
FT CHAIN 1..1883
FT /note="Endoribonuclease Dicer homolog 1"
FT /id="PRO_0000378416"
FT DOMAIN 274..413
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 629..789
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 817..912
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 1163..1296
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 1320..1498
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1538..1686
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1712..1775
FT /note="DRBM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 1797..1872
FT /note="DRBM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 71..97
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 129..188
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 221..262
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 577..604
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 901..928
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 358..361
FT /note="DECH box"
FT /evidence="ECO:0000250"
FT COMPBIAS 73..95
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 583..604
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 906..928
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 287..294
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1576
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1672
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1675
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1668
FT /note="Important for activity"
FT /evidence="ECO:0000250"
FT CONFLICT 79
FT /note="P -> T (in Ref. 5; EAZ25399)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1883 AA; 210203 MW; 0566ADA02CA424CF CRC64;
MAGGGGVGGG AGEHAAAAYW YDACEDGASL LCGIDFAASA DFDPGLIPAM DTGADDGFVA
EIDRILESIN AESSPAPPPP PPPPLPEPVP VAPPELPIQE KQLQVASAPV ANNAVAVVGV
VQRSKGVVAR KEPRRESHGC AANGGGGGEW RDGKRPRLAS GGVGGPRQEW RRRPMLPPPP
SRGWDDRRGR RDFDRVRKHE HHRREARGFW ERDRGGKMVF RSGTWEQESD REAKRARTQD
GGSMEKKAEA DRMGAAQREK PVAEERARQY QLEVLEQAKS RNTIAFLETG AGKTLIAVLL
IKSVCDKMLK ENKKMLAVFL VPKVPLVYQV LVMTAQILLN ILRHSIIKMD AIHLLILDEC
HHAVKKHPYS LVMSEFYHTT PKEKRPAVFG MTASPVNLKG VTSQEDCAIK IRNLESKLDS
VVCTIKDRKE LEKHVPMPLE VVVQYDKAAT LWSLHEQIKQ MESTVEEAAL SSSKRTKWQF
MGARDAGSRD ELRLVYGVSE RTESDGAANL IQKLRAINYA LGELGQWCAY KVAQSFLTAL
QNDERANYQV DVKFQESYLK KVVDLLHCQL TEGAAMKSET SDVEMQNTEK HNTNDLEEGE
LPDSHGEHVD EVIGAAVADG KVTPRVQALI KILLKYQHTE DFRAIIFVER VVTALVLPKV
LAELPSLSFI RCASLIGHNN NQEMRACQMQ DTISKFRDGR VTLLVATSVA EEGLDIRQCN
VVIRFDLAKT VLAYIQSRGR ARKPGSDYIL MLERGNISHE TFLRNARNSE ETLRKEAMER
TDLSHLDGTS VLSPVDTSPG SMYQVESTGA VVSLNSAVGL IHFYCSQLPS DRYSILHPEF
IMQKYEKPGG SVEYSCKLQL PCNAPFEKLE GPICSSIRLA QQAVCLAACK KLHEMGAFTD
TLLPDRGSGE GEKTEQNDEG EPLPGTARHR EFYPEGVADI LRGEWILSGR DGYQNSQFIK
LYMYSVNCVN VGTSKDPFVT QLSNFAIIFG NELDAEVLST TMDLFVARTM ITKASLVFRG
RIEITESQLV LLKSFHVRLM SIVLDVDVDP STTPWDPAKA YLFVPVGAEK CTDPLREIDW
TLVNNIVNTD AWNNPLQRAR PDVYLGTNER TLGGDRREYG FGKLRHGTAF GQKAHPTYGI
RGAIAEFDIV KASGLVPARD RGHFSDYQNQ GKLFMADSCW NAKDLAGMVV TAAHSGKRFY
VDCICYNMNA ENSFPRKEGY LGPLEYSSYA DYYKQKYGVE LIYRKQPLIR ARGVSYCKNL
LSPRFEHSDA REGDFSENLD KTYYVYLPPE LCLVHPLPGS LVRGAQRLPS IMRRVESMLL
AVQLKDIIDY PVPATKILEA LTAASCQETL CYERAELLGD AYLKWVVSRF LFLKYPQKHE
GQLTRMRQQM VSNMVLYQYA LNKTLQSYIQ ADRFAPSRWA APGVLPVFDE ESREYEPSIF
DEESTGCELQ KESYDDYADN MQEDGEIEGD SSCYRVLSSK TLADVVEALI GVYYVAGGKI
AANHLMKWIG IHAELDPEEI PPPKPYDIPE SIMRSINFDT LKGVLGIEFQ NKGLLVEAIT
HASRPSSGVS CYQRLEFVGD AVLDHLITRH LFFTYTDLPP GRLTDLRAAA VNNENFARVA
VKHKLHVHLR HGSSALETQI REFVKDVQEE LLKPGFNSFG LGDCKAPKVL GDIVESIAGA
IFLDSGYDTS VVWKVFQPLL HPMVTPETLP MHPVRELQER CQQQAEGLEY KASRAGNIAT
VEVFVDGVQI GVAQNPQKKM AQKLAARNAL VVLKEKETAT KKEDERDGEK KNGAQMFTRQ
TLNDICLRRQ WPMPQYRCVN EGGPAHAKRF VYSVRVNTSD RGWTDECIGE PMPSVKKAKD
SAAVLLLELL NRDFPDKPDG KQP
//
