DCL2B_ORYSJ
ID DCL2B_ORYSJ Reviewed; 1377 AA.
AC Q69LX2; Q0J2Q7;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Endoribonuclease Dicer homolog 2b;
DE AltName: Full=Dicer-like protein 2b;
DE Short=OsDCL2b;
DE EC=3.1.26.-;
GN Name=DCL2B; OrderedLocusNames=Os09g0315100, LOC_Os09g14610;
GN ORFNames=OSJNBa0057D11.8-1, OSJNBb0079G12.35-1;
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=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 [2]
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 [3]
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 [4]
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=BAD34005.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD36404.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF24758.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP005782; BAD34005.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP005802; BAD36404.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008215; BAF24758.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014965; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_015611517.1; XM_015756031.1.
DR AlphaFoldDB; Q69LX2; -.
DR SMR; Q69LX2; -.
DR STRING; 39947.Q69LX2; -.
DR PRIDE; Q69LX2; -.
DR GeneID; 4346696; -.
DR KEGG; osa:4346696; -.
DR InParanoid; Q69LX2; -.
DR OrthoDB; 1337630at2759; -.
DR Proteomes; UP000000763; Chromosome 9.
DR Proteomes; UP000059680; Chromosome 9.
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; 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; 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..1377
FT /note="Endoribonuclease Dicer homolog 2b"
FT /id="PRO_0000378418"
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 534..626
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 786..913
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 940..1095
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1132..1276
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1302..1367
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 1171
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1265
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1258
FT /note="Important for activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1377 AA; 154800 MW; 19BD98B5D8892DC6 CRC64;
MGGPLTAAGG RGDGGAKAVE PLRPPPPPDP KTMARWYQLE ALERAVRGNT LAFLETGSGK
TLIAVMLLRA YAHRVRRPDS RRFAVFLVPT VVLVGQQARV VEQHTDLVVK QFCGEMGVDF
WDAATWRSQL EDGEVLVMTP QILLDNLRHS FFRLQDIALL IFDECHHARG NTPYACIFKE
FYHPQLNSSA SDPLPRIFGM SASLIYSKDL NQHNYSKQIS EIENLMNSKV YTVDSESALS
EYIPFASTKI VHFDDSNISS ELHANILSCL NRLTKKHIEA LDRKLHGSSL ENAKQRISKL
HRTFVYCLYN LGVWLAAKAA EVQSYEENSL SFWGETLDKN VEGFIRNYSE EVHRELSCFL
KNGHIGEKFP ADSQDGILTP KVHCLIRTLL QYRHMQDLRC IVFVQRVITS IVLEPLLSSI
HQMSGWNVKH MAGSRPGLLS QSRKNHTEIV ESFRKGKVHI IIATQILEEG LDVPSCNLVI
RFDPSATVCS FIQSRGRARM ENSDYLLLVG RGDVEAHTNA KKFLASGQIM REESLRLGSI
SCQPLENTLC EDTYYRVEST PAFDIDKASG TCTLHLPKSS PVQTVNVEGE GSILKETVCL
KACQELHAIG ALTDSLLPEL DVPCDEEPDI VVENKIEQPS YFPEEFVDNW RSFSRLGIYY
CYKISLEGCP KTASPTDILL ALKCDLGSDF TSSSFKLPGG QDNASVTMKY VGIIHLNQEQ
VIIARRFQTT ILSFLIGDDH LEVSNGIKYF HEMQVPIGVV YLLLPLVSGR IDWCSMKFSS
SPIYEANNKH MTHCHSCRDI DLLQTKDGPF CRCILKNSIV CTPHNNIFYV ISGFLDLDAN
SRLPQHDGTV VTYKDYFKTR HGLTLTFENQ PLLAGSKHVK VRNFLHNYYY KKEKEPGDRY
SVELPPELCR IIMSPVSANN LHIFSYVPSI MFRIQCMLLS VKLKVQLGPT VQQFDVPVLK
ILEALTTKKC QEEFSQESLE TLGDSFLKYV TTRHLFSEYR LQHEGILTKM KKNLISNAAL
CQLACSSNLV GYIHAEEFNP RDWIIPCLDY DERGNKKISF LAPNGMYSQR KMSIKSKRIA
DSVEALIGAY LSTAGEKAAF LLMKSLGMNI EFHTEIPVER KISMKAEEFI DVRSLEGMLG
YKFNDSLLLL EALTHGSYQT SGPTSCYQRL EFLGDAILDH LFTEYYYSKY PDCTPELLTD
LRSASVNNNC YAHAAVKSGL NKHILHSSSE LHRKMSYYLG QSFTGPSYGW EAGIGLPKVL
GDVIESIAGA IYLDSKCDKE VVWRSMKRLL EPLATPETIE PDPVKGLQEF CDRRSFKITY
EKNHVDGVSS VIARVKAGET TYSATKSGPC KLAKKLASKA VLKDLIAGHK DTEAAAV
