DCL3A_ORYSJ
ID DCL3A_ORYSJ Reviewed; 1651 AA.
AC Q5N870; A0A0P0VC26;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Endoribonuclease Dicer homolog 3a;
DE AltName: Full=Dicer-like protein 3a;
DE Short=OsDCL3a;
DE EC=3.1.26.-;
GN Name=DCL3A; OrderedLocusNames=Os01g0909200, LOC_Os01g68120;
GN ORFNames=P0456E05.21;
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=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
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 MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP TISSUE SPECIFICITY, 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 -!- TISSUE SPECIFICITY: Expressed in roots, shoot apical meristem (SAM),
CC leaves, panicles and seeds. {ECO:0000269|PubMed:18826656}.
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00657}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AK120075; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AP003416; BAD82327.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF07062.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS75821.1; -; Genomic_DNA.
DR EMBL; AK120075; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015621462.1; XM_015765976.1.
DR AlphaFoldDB; Q5N870; -.
DR SMR; Q5N870; -.
DR STRING; 4530.OS01T0909200-01; -.
DR PRIDE; Q5N870; -.
DR EnsemblPlants; Os01t0909200-01; Os01t0909200-01; Os01g0909200.
DR GeneID; 4324864; -.
DR Gramene; Os01t0909200-01; Os01t0909200-01; Os01g0909200.
DR KEGG; osa:4324864; -.
DR eggNOG; KOG0701; Eukaryota.
DR HOGENOM; CLU_000907_4_4_1; -.
DR InParanoid; Q5N870; -.
DR OMA; TRKNHAY; -.
DR OrthoDB; 1337630at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; Q5N870; 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:0003677; F:DNA binding; IEA:InterPro.
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; IPR038248; Dicer_dimer_sf.
DR InterPro; IPR005034; Dicer_dimerisation_dom.
DR InterPro; IPR006935; Helicase/UvrB_N.
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; PF04851; ResIII; 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 2: Evidence at transcript level;
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..1651
FT /note="Endoribonuclease Dicer homolog 3a"
FT /id="PRO_0000378419"
FT DOMAIN 39..214
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 402..563
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 587..677
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 864..979
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 1413..1481
FT /note="DRBM"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 161..164
FT /note="DECH box"
FT /evidence="ECO:0000250"
FT COMPBIAS 9..25
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 52..59
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1280
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1375
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1378
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1371
FT /note="Important for activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1651 AA; 184892 MW; DDDCEB12386F4818 CRC64;
MNPLKRSLES SSQEHEAGKQ KLQKRECQDF TPRRYQLDVY EVAMRRNTIA MLDTGAGKTM
IAVMLIKEFG KINRTKNAGK VIIFLAPTVQ LVTQQCEVIE IHTDFEVEQY YGAKGVDQWT
GPRWQEQISK YQVMVMTPQV FLQALRNAFL ILDMVSLMIF DECHHATGNH PYTRIMKEFY
HKSEHKPSVF GMTASPVIRK GISSHLDCEG QFCELENLLD AKIYTVSDRE EIEFCVPSAK
EMCRYYDSKP VCFEDLSEEL GVLCSKYDAL ITELQNKRSD MYKDADDITK ESKRRLSKSI
AKICYCLDDV GLICASEATK ICIERGQEKG WLKEVVDATD QQTDANGSRL FAENSALHMK
FFEEALHLID KRLQQGIDML LNSESGCVEA AKTGYISPKL YELIQIFHSF SNSRHARCLI
FVDRKITARV IDRMIKKIGH LAHFTVSFLT GGRSSVDALT PKMQKDTLDS FRSGKVNLLF
TTDVAEEGIH VPECSCVIRF DLPRTTRSYV QSRGRARQED SQYILMIERG NVKQNDLISA
IVRSETSMVK IASSRESGNL SPGFVPNEEI NEYHVGTTGA KVTADSSISI VYRYCEKLPQ
DKCYSPKPTF EFTHHDDGYV CTLALPPSAV LQILVGPKAR NMHKAKQLVC LDACKKLHEL
GALDDHLCLS VEDPVPEIVS KNKGTGIGTT KRKELHGTTR IHAWSGNWVS KKTALKLQSY
KMNFVCDQAG QIYSEFVLLI DATLPDEVAT LEIDLYLHDK MVKTSVSSCG LLELDAQQME
QAKLFQGLLF NGLFGKLFTR SKVPNAPREF ILNKEDTFVW NTASVYLLLP TNPSFDSNVC
INWSVIDAAA TAVKLMRRIY SENKRELLGI FDSDQNVGDL IHLANKSCKA NSLKDMVVLA
VHTGKIYTAL DITELSGDSA FDGASDKKEC KFRTFAEYFK KKYGIVLRHP SQPLLVLKPS
HNPHNLLSSK FRDEGNVVEN MSNGTPVVNK TSNRVHMPPE LLIPLDLPVE ILRSFYLFPA
LMYRIESLTL ASQLRSEIGY SDSNISSFLI LEAITTLRCS EDFSMERLEL LGDSVLKYAV
SCHLFLKFPN KDEGQLSSIR CHMICNATLY KLGIERNVQG YVRDAAFDPR RWLAPGQLSI
RPSPCECPVK SEVVTDDIHI IDDKAIVLGK ACDKGHRWMC SKTIADCVEA IIGAYYAGGG
LRAAMAVLKW LGIGAEIEED LIVQAILSAS VQTYLPKDNV FEMLEAKLGY SFSVKGLLVE
ALTHPSQQEL GAKYCYERLE FLGDAVLDIL LTRYLFNSHK DTNEGELTDL RSASVNNENF
AQVAVKHNFH HFLQHSSGLL LDQITEYVNR LEGSSMDKVE LLSDGLPKGP KVLGDIVESI
AGAILLDTKL DLDVVWGIFE PLLSPIVTPE NLELPPYREL IEWCGKHGYF VGINCRDQGD
TVVATLDVQL KEVLLVRQGF SKKRKDAKAH ASSLLLKDLE EKGLIIPKNA SKTEQFEKHC
GSTNPFNNLH VDAMDTQTPK PTKEKNAADS RNISDPLLGK PLHVIVKTSK GGPRIALYEL
CKKLQWPMPT MESEKVQPSF SSVCSSPGGS SQKATPQAFA FASTITLHIP NADVISLTGD
GRADKKSSQD SAALFLLYEL QRRGTLQLQE V
