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DCL1_ORYSJ
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   03-AUG-2022, entry version 144.
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; 4530.OS03T0121901-00; -.
DR   PaxDb; Q8LMR2; -.
DR   PRIDE; 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:0010445; C:nuclear dicing body; IEA:EnsemblPlants.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003725; F:double-stranded RNA binding; IEA:EnsemblPlants.
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:0000911; P:cytokinesis by cell plate formation; IEA:EnsemblPlants.
DR   GO; GO:0009880; P:embryonic pattern specification; IEA:EnsemblPlants.
DR   GO; GO:0010599; P:lsiRNA processing; IEA:EnsemblPlants.
DR   GO; GO:0035196; P:miRNA processing; IMP:UniProtKB.
DR   GO; GO:0035279; P:miRNA-mediated gene silencing by mRNA destabilization; IEA:EnsemblPlants.
DR   GO; GO:2000034; P:regulation of seed maturation; IEA:EnsemblPlants.
DR   GO; GO:0009616; P:RNAi-mediated antiviral immune response; IEA:EnsemblPlants.
DR   GO; GO:0048317; P:seed morphogenesis; IEA:EnsemblPlants.
DR   GO; GO:0030422; P:siRNA processing; IBA:GO_Central.
DR   GO; GO:0010267; P:ta-siRNA processing; IEA:EnsemblPlants.
DR   GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IEA:EnsemblPlants.
DR   CDD; cd00593; RIBOc; 2.
DR   Gene3D; 1.10.1520.10; -; 2.
DR   Gene3D; 3.30.160.380; -; 1.
DR   Gene3D; 3.40.50.300; -; 3.
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   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; SSF101690; SSF101690; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   SUPFAM; SSF69065; SSF69065; 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          1156..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
 
 
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