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DCL2_ARATH
ID   DCL2_ARATH              Reviewed;        1388 AA.
AC   Q3EBC8; Q1KL57; Q1KL58; Q9M9P8;
DT   08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT   15-JAN-2008, sequence version 2.
DT   03-AUG-2022, entry version 129.
DE   RecName: Full=Endoribonuclease Dicer homolog 2;
DE            EC=3.1.26.-;
DE   AltName: Full=Dicer-like protein 2;
DE            Short=AtDCL2;
GN   OrderedLocusNames=At3g03300; ORFNames=T17B22.1;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
RX   PubMed=16638569; DOI=10.1016/j.febslet.2006.03.072;
RA   Margis R., Fusaro A.F., Smith N.A., Curtin S.J., Watson J.M.,
RA   Finnegan E.J., Waterhouse P.M.;
RT   "The evolution and diversification of Dicers in plants.";
RL   FEBS Lett. 580:2442-2450(2006).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130713; DOI=10.1038/35048706;
RA   Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA   Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA   Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA   Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA   Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA   Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA   Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA   Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA   Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA   Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA   Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA   de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA   Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA   Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA   Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA   Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA   Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA   Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA   Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA   Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA   Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA   Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA   Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT   "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL   Nature 408:820-822(2000).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   SUBCELLULAR LOCATION.
RX   PubMed=15024409; DOI=10.1371/journal.pbio.0020104;
RA   Xie Z., Johansen L.K., Gustafson A.M., Kasschau K.D., Lellis A.D.,
RA   Zilberman D., Jacobsen S.E., Carrington J.C.;
RT   "Genetic and functional diversification of small RNA pathways in plants.";
RL   PLoS Biol. 2:E104-E104(2004).
RN   [5]
RP   FUNCTION.
RX   PubMed=16040244; DOI=10.1016/j.cub.2005.07.024;
RA   Gasciolli V., Mallory A.C., Bartel D.P., Vaucheret H.;
RT   "Partially redundant functions of Arabidopsis DICER-like enzymes and a role
RT   for DCL4 in producing trans-acting siRNAs.";
RL   Curr. Biol. 15:1494-1500(2005).
RN   [6]
RP   FUNCTION.
RX   PubMed=16810317; DOI=10.1038/sj.emboj.7601217;
RA   Bouche N., Lauressergues D., Gasciolli V., Vaucheret H.;
RT   "An antagonistic function for Arabidopsis DCL2 in development and a new
RT   function for DCL4 in generating viral siRNAs.";
RL   EMBO J. 25:3347-3356(2006).
RN   [7]
RP   FUNCTION.
RX   PubMed=17586651; DOI=10.1105/tpc.106.047449;
RA   Diaz-Pendon J.A., Li F., Li W.X., Ding S.W.;
RT   "Suppression of antiviral silencing by cucumber mosaic virus 2b protein in
RT   Arabidopsis is associated with drastically reduced accumulation of three
RT   classes of viral small interfering RNAs.";
RL   Plant Cell 19:2053-2063(2007).
RN   [8]
RP   FUNCTION.
RX   PubMed=17592042; DOI=10.1261/rna.541307;
RA   Moissiard G., Parizotto E.A., Himber C., Voinnet O.;
RT   "Transitivity in Arabidopsis can be primed, requires the redundant action
RT   of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by
RT   viral-encoded suppressor proteins.";
RL   RNA 13:1268-1278(2007).
RN   [9]
RP   FUNCTION.
RX   PubMed=18353962; DOI=10.1128/jvi.00272-08;
RA   Donaire L., Barajas D., Martinez-Garcia B., Martinez-Priego L., Pagan I.,
RA   Llave C.;
RT   "Structural and genetic requirements for the biogenesis of tobacco rattle
RT   virus-derived small interfering RNAs.";
RL   J. Virol. 82:5167-5177(2008).
RN   [10]
RP   FUNCTION.
RX   PubMed=18335032; DOI=10.1371/journal.pone.0001755;
RA   Mlotshwa S., Pruss G.J., Peragine A., Endres M.W., Li J., Chen X.,
RA   Poethig R.S., Bowman L.H., Vance V.;
RT   "DICER-LIKE2 plays a primary role in transitive silencing of transgenes in
RT   Arabidopsis.";
RL   PLoS ONE 3:E1755-E1755(2008).
RN   [11]
RP   GENE FAMILY.
RX   PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA   Xu R., Zhang S., Huang J., Zheng C.;
RT   "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT   in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT   sativa.";
RL   PLoS ONE 8:E78982-E78982(2013).
CC   -!- FUNCTION: Ribonuclease (RNase) III involved in RNA-mediated post-
CC       transcriptional gene silencing (PTGS). Involved in the processing of
CC       natural small interfering RNAs (nat-siRNAs, derived from cis-natural
CC       antisense transcripts) by cleaving small dsRNAs into 24 nucleotide nat-
CC       siRNAs. Plays an essential role in transitive silencing of transgenes
CC       by processing secondary siRNAs. This pathway, which requires DCL4 and
CC       RDR6, amplifies silencing by using the target RNA as substrate to
CC       generate secondary siRNAs, providing an efficient mechanism for long-
CC       distance silencing. May participate with DCL3 in the production of 24
CC       nucleotide repeat-associated siRNAs (ra-siRNAs) which derive from
CC       heterochromatin and DNA repeats such as transposons. Plays a role in
CC       antiviral RNA silencing. Involved in the production of viral siRNAs
CC       derived from the turnip crinkle virus (TCV) and tobacco rattle virus
CC       (TRV). Targeted by the viral silencing suppressor (VSR) protein 2b of
CC       the cucumber mosaic virus (CMV) that inactivates DCL2 function in RNA
CC       silencing. Does not seem to be involved in microRNAs (miRNAs)
CC       processing. {ECO:0000269|PubMed:16040244, ECO:0000269|PubMed:16810317,
CC       ECO:0000269|PubMed:17586651, ECO:0000269|PubMed:17592042,
CC       ECO:0000269|PubMed:18335032, ECO:0000269|PubMed:18353962}.
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   -!- INTERACTION:
CC       Q3EBC8; O04492: DRB1; NbExp=2; IntAct=EBI-2464030, EBI-632620;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15024409}. Cytoplasm
CC       {ECO:0000269|PubMed:15024409}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q3EBC8-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q3EBC8-2; Sequence=VSP_040615;
CC   -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC       {ECO:0000255|PROSITE-ProRule:PRU00657}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAF26098.1; Type=Erroneous gene model prediction; Note=The predicted gene At3g03300 has been split into 2 genes: At3g03300 and At3g03305.; Evidence={ECO:0000305};
CC       Sequence=ABF19797.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; DQ479970; ABF19797.1; ALT_INIT; mRNA.
DR   EMBL; DQ479971; ABF19798.1; -; mRNA.
DR   EMBL; AC012328; AAF26098.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002686; AEE73924.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE73925.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE73926.1; -; Genomic_DNA.
DR   RefSeq; NP_001078101.1; NM_001084632.1. [Q3EBC8-2]
DR   RefSeq; NP_001189798.1; NM_001202869.2. [Q3EBC8-1]
DR   RefSeq; NP_566199.4; NM_111200.5. [Q3EBC8-1]
DR   AlphaFoldDB; Q3EBC8; -.
DR   SMR; Q3EBC8; -.
DR   IntAct; Q3EBC8; 4.
DR   STRING; 3702.AT3G03300.1; -.
DR   iPTMnet; Q3EBC8; -.
DR   PaxDb; Q3EBC8; -.
DR   PRIDE; Q3EBC8; -.
DR   ProteomicsDB; 224607; -. [Q3EBC8-1]
DR   EnsemblPlants; AT3G03300.1; AT3G03300.1; AT3G03300. [Q3EBC8-1]
DR   EnsemblPlants; AT3G03300.2; AT3G03300.2; AT3G03300. [Q3EBC8-2]
DR   EnsemblPlants; AT3G03300.3; AT3G03300.3; AT3G03300. [Q3EBC8-1]
DR   GeneID; 821300; -.
DR   Gramene; AT3G03300.1; AT3G03300.1; AT3G03300. [Q3EBC8-1]
DR   Gramene; AT3G03300.2; AT3G03300.2; AT3G03300. [Q3EBC8-2]
DR   Gramene; AT3G03300.3; AT3G03300.3; AT3G03300. [Q3EBC8-1]
DR   KEGG; ath:AT3G03300; -.
DR   Araport; AT3G03300; -.
DR   TAIR; locus:2097705; AT3G03300.
DR   eggNOG; KOG0701; Eukaryota.
DR   HOGENOM; CLU_000907_4_4_1; -.
DR   InParanoid; Q3EBC8; -.
DR   OMA; HFCAVIP; -.
DR   OrthoDB; 1337630at2759; -.
DR   PhylomeDB; Q3EBC8; -.
DR   PRO; PR:Q3EBC8; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q3EBC8; baseline and differential.
DR   Genevisible; Q3EBC8; AT.
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:0051607; P:defense response to virus; IMP:TAIR.
DR   GO; GO:0010216; P:maintenance of DNA methylation; IMP:TAIR.
DR   GO; GO:0051214; P:RNAi-mediated antiviral immunity against RNA virus; IGI:TAIR.
DR   GO; GO:0030422; P:siRNA processing; IBA:GO_Central.
DR   GO; GO:0010267; P:ta-siRNA processing; IMP:TAIR.
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   1: Evidence at protein level;
KW   Alternative splicing; ATP-binding; Cytoplasm; Endonuclease; Helicase;
KW   Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease;
KW   Nucleotide-binding; Nucleus; Plant defense; Reference proteome; Repeat;
KW   RNA-binding; RNA-mediated gene silencing.
FT   CHAIN           1..1388
FT                   /note="Endoribonuclease Dicer homolog 2"
FT                   /id="PRO_0000404660"
FT   DOMAIN          31..210
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   DOMAIN          380..544
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT   DOMAIN          559..645
FT                   /note="Dicer dsRNA-binding fold"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT   DOMAIN          807..935
FT                   /note="PAZ"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT   DOMAIN          962..1113
FT                   /note="RNase III 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT   DOMAIN          1149..1296
FT                   /note="RNase III 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT   DOMAIN          1315..1384
FT                   /note="DRBM"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT   MOTIF           152..155
FT                   /note="DECH box"
FT   BINDING         44..51
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   BINDING         1188
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         1282
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         1285
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   SITE            1278
FT                   /note="Important for activity"
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         1..83
FT                   /note="MTMDADAMETETTDQVSASPLHFARSYQVEALEKAIKQNTIVFLETGSGKTL
FT                   IAIMLLRSYAYLFRKPSPCFCVFLVPQVVLV -> MLLCLLGSSSGSCHSGIGVRIGVV
FT                   DKGIHQYTDLSFVLQFLHYYTCSFSKFRNFSVTFSIISAFFLVCF (in isoform
FT                   2)"
FT                   /evidence="ECO:0000303|PubMed:16638569"
FT                   /id="VSP_040615"
FT   CONFLICT        511
FT                   /note="L -> S (in Ref. 1; ABF19797/ABF19798)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        693
FT                   /note="F -> L (in Ref. 1; ABF19797/ABF19798)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        738
FT                   /note="Q -> R (in Ref. 1; ABF19797/ABF19798)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1130
FT                   /note="F -> L (in Ref. 1; ABF19797/ABF19798)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1388 AA;  156865 MW;  385D5A28E048B10D CRC64;
     MTMDADAMET ETTDQVSASP LHFARSYQVE ALEKAIKQNT IVFLETGSGK TLIAIMLLRS
     YAYLFRKPSP CFCVFLVPQV VLVTQQAEAL KMHTDLKVGM YWGDMGVDFW DSSTWKQEVD
     KYEVLVMTPA ILLDALRHSF LSLSMIKVLI VDECHHAGGK HPYACIMREF YHKELNSGTS
     NVPRIFGMTA SLVKTKGENL DSYWKKIHEL ETLMNSKVYT CENESVLAGF VPFSTPSFKY
     YQHIKIPSPK RASLVEKLER LTIKHRLSLG TLDLNSSTVD SVEKRLLRIS STLTYCLDDL
     GILLAQKAAQ SLSASQNDSF LWGELNMFSV ALVKKFCSDA SQEFLAEIPQ GLNWSVANIN
     GNAEAGLLTL KTVCLIETLL GYSSLENIRC IIFVDRVITA IVLESLLAEI LPNCNNWKTK
     YVAGNNSGLQ NQTRKKQNEI VEDFRRGLVN IIVATSILEE GLDVQSCNLV IRFDPASNIC
     SFIQSRGRAR MQNSDYLMMV ESGDLLTQSR LMKYLSGGKR MREESLDHSL VPCPPLPDDS
     DEPLFRVEST GATVTLSSSV SLIYHYCSRL PSDEYFKPAP RFDVNKDQGS CTLYLPKSCP
     VKEVKAEANN KVLKQAVCLK ACIQLHKVGA LSDHLVPDMV VAETVSQKLE KIQYNTEQPC
     YFPPELVSQF SAQPETTYHF YLIRMKPNSP RNFHLNDVLL GTRVVLEDDI GNTSFRLEDH
     RGTIAVTLSY VGAFHLTQEE VLFCRRFQIT LFRVLLDHSV ENLMEALNGL HLRDGVALDY
     LLVPSTHSHE TSLIDWEVIR SVNLTSHEVL EKHENCSTNG ASRILHTKDG LFCTCVVQNA
     LVYTPHNGYV YCTKGVLNNL NGNSLLTKRN SGDQTYIEYY EERHGIQLNF VDEPLLNGRH
     IFTLHSYLHM AKKKKEKEHD REFVELPPEL CHVILSPISV DMIYSYTFIP SVMQRIESLL
     IAYNLKKSIP KVNIPTIKVL EAITTKKCED QFHLESLETL GDSFLKYAVC QQLFQHCHTH
     HEGLLSTKKD GMISNVMLCQ FGCQQKLQGF IRDECFEPKG WMVPGQSSAA YSLVNDTLPE
     SRNIYVASRR NLKRKSVADV VESLIGAYLS EGGELAALMF MNWVGIKVDF TTTKIQRDSP
     IQAEKLVNVG YMESLLNYSF EDKSLLVEAL THGSYMMPEI PRCYQRLEFL GDSVLDYLIT
     KHLYDKYPCL SPGLLTDMRS ASVNNECYAL VAVKANLHKH ILYASHHLHK HISRTVSEFE
     QSSLQSTFGW ESDISFPKVL GDVIESLAGA IFVDSGYNKE VVFASIKPLL GCMITPETVK
     LHPVRELTEL CQKWQFELSK AKDFDSFTVE VKAKEMSFAH TAKASDKKMA KKLAYKEVLN
     LLKNSLDY
 
 
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