DCL3B_ORYSJ
ID DCL3B_ORYSJ Reviewed; 1637 AA.
AC Q7XD96; Q0IWV3; Q8W367;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Endoribonuclease Dicer homolog 3b;
DE AltName: Full=Dicer-like protein 3b;
DE Short=OsDCL3b;
DE EC=3.1.26.-;
GN Name=DCL3B; OrderedLocusNames=Os10g0485600, LOC_Os10g34430;
GN ORFNames=OSJNBa0029C15.23;
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=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
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 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).
CC -!- FUNCTION: Probably involved in the RNA silencing pathway. May cleave
CC double-stranded RNA to produce short 21-24 nucleotides (nt) RNAs which
CC target the selective destruction of complementary RNAs (By similarity).
CC {ECO:0000250}.
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 -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00657}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL59041.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAP54346.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF26812.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC087182; AAL59041.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000086; AAP54346.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008216; BAF26812.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014966; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR AlphaFoldDB; Q7XD96; -.
DR SMR; Q7XD96; -.
DR STRING; 4530.OS10T0485600-00; -.
DR PaxDb; Q7XD96; -.
DR PRIDE; Q7XD96; -.
DR EnsemblPlants; Os10t0485600-01; Os10t0485600-01; Os10g0485600.
DR Gramene; Os10t0485600-01; Os10t0485600-01; Os10g0485600.
DR eggNOG; KOG0701; Eukaryota.
DR HOGENOM; CLU_000907_4_4_1; -.
DR InParanoid; Q7XD96; -.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR Genevisible; Q7XD96; OS.
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:0035194; P:post-transcriptional gene silencing by RNA; IEA:UniProt.
DR GO; GO:0030422; P:siRNA processing; IBA:GO_Central.
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; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR038248; Dicer_dimer_sf.
DR InterPro; IPR005034; Dicer_dimerisation_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; PF00270; DEAD; 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; 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; 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..1637
FT /note="Endoribonuclease Dicer homolog 3b"
FT /id="PRO_0000378420"
FT DOMAIN 46..222
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 404..556
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 581..671
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 867..1006
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 1031..1200
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1241..1389
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1412..1481
FT /note="DRBM 1"
FT DOMAIN 1545..1629
FT /note="DRBM 2"
FT REGION 1..40
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 169..172
FT /note="DECH box"
FT COMPBIAS 7..23
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 59..66
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1214
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1309
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1312
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1305
FT /note="Important for activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1637 AA; 184725 MW; 811F2AB02659B318 CRC64;
MADDEAAVLP PPPPLPPPCR PHRQLRPRGS RPTADTTPRT SQLVEVFEAA LRGNTIAVLD
TGSGKTMVAV MLAREHARRV RAGEAPRRIV VFLAPTVHLV HQQFEVIREY TDLDVMMCSG
ASRVGEWGAD HWKEEVGRNE IVVMTPQILL DALRHAFLTM SAVSLLIFDE CHRACGSHPY
ARIMKEFYFG SQWRPDVFGM TASPVATKGA STLHNCEAHI SQLELTLDAK IYIVEDRNEL
ESFSPPTTIV NKYYDAYMVD FDNLKSKLQI FSDEFDSLLV GLQESPSNKF KDTDNILETS
RKSLSRYHGK ILYSLNDLGP IITSEVVKIH IESVKPLCDS EDCIFSKASL CLHMSYFKEA
LSLIEEILPQ GYGELMKSES GSEELTKRGY ISSKVNTLIN IFKSFGSSNE VLCLIFVDRI
ITAKAVERFM RGIVNFSCFS ISYLTGGSTS KDALSPAVQR FTLDLFRAGK VNLLFTTDVT
EEGVDVPNCS CVIRFDLPRT VCSYVQSRGR ARRNNSEFIL MIERGNLQQQ EHIFRMIQTG
YYVKNCALYR HPNALSYDLS IQGMYTYQVQ STGATITADC CVNLIRKYCE KLPKDRYFMP
KPSFEVTIED GLFKCTLTLP RNAAFQSIVG PLSSSSNLSK QLVSLEACKK LHQLGELNDH
LVPLTEEPMD TDFTTADEKC ISGPGTTKRK ELHGTTCVLA LSGTWIHDSE NITLNTYRID
FLCDQEGENY AGFVLLMEPE LDDDVAPSKM DLFLIPNKMV YTTVTPRGKV QLNKKQLGKG
KLFQEFFFNG IFGRLFHGSR KSGAQRDFIF KKGHEIQWNT ESMYLLLPLR DSSYIQDDLS
IHWEAIESCA GAVEQLWSSY QGDENVIPVN CIPQKRRGGQ EEIIHLANKS LHCSSIKDSV
VLSLHTGRIY TVLDLILDTT AEDSFDEMCK GKASPFTSFV DYYHQKYGII IQHPEQPLLL
LKQSHNAHNL LFSKLKYLDG STGKPLLMEK EQIHARVPPE LLIHLDVTTD ILKSFYLLPS
VIHRLQSLML ASQLRREIGY NQHIPVTLIL EAITTLRCCE TFSLERLELL GDSVLKYVVG
CDLFLRYPMK HEGQLSDMRS KAVCNATLHK HGIWRSLQGY VRDNAFDPRR WVAPGQISLR
PFPCNCGIET AFVPSHRRYI RDDPSFFVGK PCDRGHRWMC SKTISDCVEA LVGAYYVGGG
IAAALWVMRW FGIDIKCDMK LLQEVKFNAS HLCSLSKIND IEELEAKLKY NFSVKGLLLE
AITHPSLQEL GVDYCYQRLE FLGDSVLDLL LTRHLYATHT DVDPGELTDL RSALVSNENF
AQAVVRNNIH SHLQHGSGIL LEQITEYVRS NLECQGKESE FLQHTTCKVP KVLGDIMESI
AGAVFIDTDF NVDMVWEIFE PLLSPLITPD KLALPPYREL LELCSHIGCF LNSKCTSKGE
EVIIEMSLQL RDELLVAQGH DRNKKRAKAK AASRILADLK QQGLSIKQCL SKAKQLDIVT
SDLQFDLTSS GTQLSYSDLN DYHILEGLSS VKKEVVLPLK MEKGGPRSAL FKLCKILQWP
MPEFEFVEQR FRTPIVMDGA TTTNFNSFVS TITLHIPDAT TITFQGERRT DKKSAQDSAS
LMMLHKLQEL KICICKT
