DCL2A_ORYSJ
ID DCL2A_ORYSJ Reviewed; 1410 AA.
AC Q10HL3; A0A0P0VZP1; Q75IB0; Q75IB1; Q75IB2;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Endoribonuclease Dicer homolog 2a;
DE AltName: Full=Dicer-like protein 2a;
DE Short=OsDCL2a;
DE EC=3.1.26.-;
GN Name=DCL2A; OrderedLocusNames=Os03g0583900, LOC_Os03g38740;
GN ORFNames=OJ1785_A05.30;
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 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 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=AAS07188.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAS07189.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAS07190.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC133333; AAS07188.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC133333; AAS07189.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC133333; AAS07190.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000009; ABF97330.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF12478.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS85077.1; -; Genomic_DNA.
DR EMBL; AK072334; BAG92928.1; -; mRNA.
DR RefSeq; XP_015630302.1; XM_015774816.1.
DR AlphaFoldDB; Q10HL3; -.
DR SMR; Q10HL3; -.
DR STRING; 4530.OS03T0583900-01; -.
DR PaxDb; Q10HL3; -.
DR PRIDE; Q10HL3; -.
DR EnsemblPlants; Os03t0583900-01; Os03t0583900-01; Os03g0583900.
DR GeneID; 4333337; -.
DR Gramene; Os03t0583900-01; Os03t0583900-01; Os03g0583900.
DR KEGG; osa:4333337; -.
DR eggNOG; KOG0701; Eukaryota.
DR HOGENOM; CLU_000907_4_4_1; -.
DR InParanoid; Q10HL3; -.
DR OMA; HFCAVIP; -.
DR OrthoDB; 1337630at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q10HL3; baseline and differential.
DR Genevisible; Q10HL3; 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; 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; 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; SM00358; DSRM; 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; PS50137; DS_RBD; 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..1410
FT /note="Endoribonuclease Dicer homolog 2a"
FT /id="PRO_0000378417"
FT DOMAIN 41..222
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 388..561
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 569..655
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 815..942
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 969..1124
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1161..1308
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1334..1400
FT /note="DRBM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 163..166
FT /note="DECH box"
FT /evidence="ECO:0000250"
FT BINDING 54..61
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1200
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1294
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1297
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1290
FT /note="Important for activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1410 AA; 158494 MW; 7B092E0ED9401277 CRC64;
MGGPLTAAGG RGDGGAKAVE PLRPPPPPDP KTMARWYQLE ALERAVRGNT LAFLETGSGK
TLIAVMLLRA YAHRVRRPDS RRFAVFLVPT VVLVGQQARV VEQHTDLVVK QFCGEMGVDF
WDAATWRSQL EDGEVLVMTP QILLDNLRHS FFRLQDIALL IFDECHHARG NTPYACIFKE
FYHPQLNSSA SDPLPRIFGM SASLIYSKDL NPHNYSKQIS EIENLMNSKV YTVDSESALS
EYIPFASTKI VDFDDSNISS ELHANILSCL NRLNKKHIEA LDRKLHGSSL ENAKQRISKL
HHTFVYCLYN LGVWLAAKAA EVQSYEENSL SFWGETLDKN VEGFIRNYSE EVHRELSCFL
KNGHIGEKFP ADSQDGILTP KVHCLIRTLL QYRHMQDLRC IVFVERVITS IVLEHLLSSI
HQMSGWNVKH MAGSRPGLLS QSRKNHTEIV ESFRKGKVHI IIATQILEEG LDVPSCNLVI
RFDPSATVCS FIQSRGRARM ENSDYLLLVG RGDVEAQTNA EKFLASGQIM REESLRLGSI
SCQPLENTLC EDTYYRVEST RAIVTLNSSV PLIHFFCSKL PSDEYFNPLP RFDIDKASGT
CTLHLPKSSP VQTVNVEGEG SILKETVCLK ACQELHAIGA LTDSLLPELD VPCDEEPDIV
VENKIEQPSY FPEEFVDNWR SFSRLGIYYC YKISLEGCPK TASPTDILLA LKCDLGSDFT
SSSFKLPGGQ DNASVTMKYV GIIHLNQEQV IIARRFQTTI LSFLIGDDHL EVSNGIKYFH
EMQVPIGVVY LLLPLVSGRI DWCSMKFSSS PIYEANNKHM THCHSCKDID LLQTKDGPFC
RCILKNSIVC TPHNNIFYVI SGFLDLDANS CLPQHDGTVV TYKDYFKTRH GLTLTFENQP
LLAGSKHVKV RNFLHNCYSK KEKEPGDRYS VELPPELCRI IMSPVSANNL HIFSYVPSIM
FRIQCMLLSV KLKVQLGPTV QQFDVPVLKI LEALTTKKCQ EEFSQESLET LGDSFLKYVT
TRHLFSEYRL QHEGILTKMK KNLISNAALC QLACSSNLVG YIHAEEFNPR DWIIPCLDYD
ERDNKKISFL APNGMYSQRK MSIKSKRIAD SVEALIGAYL STAGEKAAFL LMKSLGMNIE
FHTEIPVERK ISMKAEEFIN VRSLEGMLGY KFNDSLLLLE ALTHGSYQTS GPTSCYQRLE
FLGDAILDHL FTEYYYSKYP DCTPELLTDL RSASVNNNCY AHAAVKSGLN KHILHSSSEL
HRKMSYYLEE FGQSFTGPSY GWEAGIGLPK VLGDVIESIA GAIYLDSKCD KEVVWRSMKR
LLEPLATPET IEPDPVKGLQ EFCDRRSFKI TYEKNHVDGV SSVIARVKAG ETTYSATKSG
PCKLVAKKLA SKAVLKDLIA GHKDTEAAAV
