SDE3_ARATH
ID SDE3_ARATH Reviewed; 1002 AA.
AC Q8GYD9; Q94KS1; Q9LR48;
DT 19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Probable RNA helicase SDE3;
DE EC=3.6.4.13;
DE AltName: Full=Silencing defective protein 3;
GN Name=SDE3; OrderedLocusNames=At1g05460; ORFNames=T25N20.11, T25N20.26;
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 [GENOMIC DNA], AND FUNCTION.
RX PubMed=11296239; DOI=10.1093/emboj/20.8.2069;
RA Dalmay T., Horsefield R., Braunstein T.H., Baulcombe D.C.;
RT "SDE3 encodes an RNA helicase required for post-transcriptional gene
RT silencing in Arabidopsis.";
RL EMBO J. 20:2069-2078(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=11495769; DOI=10.1016/s1360-1385(01)02040-4;
RA Willmann M.R.;
RT "Unravelling PTGS: SDE3 - an RNA helicase involved in RNA silencing in
RT Arabidopsis.";
RL Trends Plant Sci. 6:344-345(2001).
RN [6]
RP FUNCTION.
RX PubMed=12941703; DOI=10.1093/emboj/cdg431;
RA Himber C., Dunoyer P., Moissiard G., Ritzenthaler C., Voinnet O.;
RT "Transitivity-dependent and -independent cell-to-cell movement of RNA
RT silencing.";
RL EMBO J. 22:4523-4533(2003).
RN [7]
RP FUNCTION, SUBUNIT, INTERACTION WITH AGO1 AND AGO4, MUTAGENESIS OF LYS-427
RP AND TRP-888, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=22940249; DOI=10.1016/j.molcel.2012.07.028;
RA Garcia D., Garcia S., Pontier D., Marchais A., Renou J.P., Lagrange T.,
RA Voinnet O.;
RT "Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral
RT defense and silencing of nonconserved intergenic regions.";
RL Mol. Cell 48:109-120(2012).
RN [8]
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: Probable RNA helicase required for post-transcriptional gene
CC silencing (PTGS), a process that provides protection in plants against
CC virus infection and can suppress expression of transgenes. Plays a
CC central role in RNA interference (RNAi) process, a process that
CC mediates mRNA destruction of translational repression. Required for the
CC assembly of the RISC complex, a complex required for target RNA
CC destruction or repression. May be required in the RISC assembly to
CC unwind miRNAs, in the production of single-stranded miRNA from the
CC double-stranded miRNA, a key step in RISC formation. Involved in the
CC amplification of sense-PTGS (S-PTGS), leading to siRNA production.
CC Required for the maintenance but not the initiation of tobacco rattle
CC virus (TRV)-mediated silencing, probably by mediating/maintaining DNA
CC methylation and chromatin-based transcriptional gene silencing at some
CC genomic locations. {ECO:0000269|PubMed:11296239,
CC ECO:0000269|PubMed:11495769, ECO:0000269|PubMed:12941703,
CC ECO:0000269|PubMed:22940249}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC -!- SUBUNIT: Interacts with AGO1 and AGO2. {ECO:0000269|PubMed:22940249}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Delayed loss of transgene silencing (post-
CC transcriptional gene silencing (PTGS)), with full silencing in the
CC cotyledons and in the hypocotyl, contrasting with a loss of silencing
CC in true leaves. Impaired maintenance of tobacco rattle virus (TRV)-
CC mediated silencing. Reduced methylation of cytosine residues in targets
CC loci but enrichment of histone-H3 'Lys-4' methylation (H3K4me3) at the
CC same sites. {ECO:0000269|PubMed:11495769, ECO:0000269|PubMed:22940249}.
CC -!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family. SDE3 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF79736.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF339908; AAK40099.1; -; Genomic_DNA.
DR EMBL; AC005106; AAF79736.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27843.1; -; Genomic_DNA.
DR EMBL; AK117698; BAC42350.1; -; mRNA.
DR PIR; C86189; C86189.
DR RefSeq; NP_172037.1; NM_100425.4.
DR AlphaFoldDB; Q8GYD9; -.
DR SMR; Q8GYD9; -.
DR BioGRID; 22289; 1.
DR STRING; 3702.AT1G05460.1; -.
DR iPTMnet; Q8GYD9; -.
DR PaxDb; Q8GYD9; -.
DR PRIDE; Q8GYD9; -.
DR ProteomicsDB; 232718; -.
DR EnsemblPlants; AT1G05460.1; AT1G05460.1; AT1G05460.
DR GeneID; 837047; -.
DR Gramene; AT1G05460.1; AT1G05460.1; AT1G05460.
DR KEGG; ath:AT1G05460; -.
DR Araport; AT1G05460; -.
DR TAIR; locus:2200996; AT1G05460.
DR eggNOG; KOG1804; Eukaryota.
DR HOGENOM; CLU_001666_6_3_1; -.
DR InParanoid; Q8GYD9; -.
DR OrthoDB; 286011at2759; -.
DR PhylomeDB; Q8GYD9; -.
DR PRO; PR:Q8GYD9; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8GYD9; baseline and differential.
DR Genevisible; Q8GYD9; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0043186; C:P granule; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; ISS:TAIR.
DR GO; GO:0035194; P:post-transcriptional gene silencing by RNA; IMP:UniProtKB.
DR GO; GO:0009616; P:RNAi-mediated antiviral immune response; IMP:TAIR.
DR CDD; cd18808; SF1_C_Upf1; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR045055; DNA2/NAM7-like.
DR InterPro; IPR041679; DNA2/NAM7-like_C.
DR InterPro; IPR041677; DNA2/NAM7_AAA_11.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR10887; PTHR10887; 1.
DR Pfam; PF13086; AAA_11; 2.
DR Pfam; PF13087; AAA_12; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Helicase; Hydrolase; Nucleotide-binding;
KW Reference proteome; RNA-mediated gene silencing.
FT CHAIN 1..1002
FT /note="Probable RNA helicase SDE3"
FT /id="PRO_0000080709"
FT REGION 831..1002
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 871..1001
FT /note="GW-rich, involved in binding to AGO proteins"
FT MOTIF 545..548
FT /note="DEAG box"
FT COMPBIAS 837..892
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 905..928
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 937..1002
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 421..428
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT MUTAGEN 427
FT /note="K->A: Loss of helicase activity."
FT /evidence="ECO:0000269|PubMed:22940249"
FT MUTAGEN 888
FT /note="W->F: Loss of binding to AGO1 and AGO4."
FT /evidence="ECO:0000269|PubMed:22940249"
FT CONFLICT 329
FT /note="M -> L (in Ref. 1; AAK40099)"
FT /evidence="ECO:0000305"
FT CONFLICT 535
FT /note="N -> K (in Ref. 1; AAK40099)"
FT /evidence="ECO:0000305"
FT CONFLICT 646
FT /note="D -> E (in Ref. 1; AAK40099)"
FT /evidence="ECO:0000305"
FT CONFLICT 991
FT /note="A -> G (in Ref. 1; AAK40099)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1002 AA; 113363 MW; 32D906F7FA95C0A5 CRC64;
MSVSGYKSDD EYSVIADKGE IGFIDYQNDG SSGCYNPFDE GPVVVSVPFP FKKEKPQSVT
VGETSFDSFT VKNTMDEPVD LWTKIYASNP EDSFTLSILK PPSKDSDLKE RQCFYETFTL
EDRMLEPGDT LTIWVSCKPK DIGLHTTVVT VDWGSDRVER VVFLLAEDKI SSSLTSNRPY
SRSRRAPKKD FAVDDYVKGS RPSKVVERSF RNRLPLYEIP KEIREMIENK EFPDDLNEGL
TARNYANYYK TLLIMEELQL EEDMRAYDME NVSMKRRGIY LSLEVPGLAE RRPSLVHGDF
IFVRHAYDDG TDHAYQGFVH RVEADEVHMK FASEFHQRHT AGSVYNVRFT YNRINTRRLY
QAVDAAEMLD PNFLFPSLHS GKRMIKTKPF VPISPALNAE QICSIEMVLG CKGAPPYVIH
GPPGTGKTMT LVEAIVQLYT TQRNARVLVC APSNSAADHI LEKLLCLEGV RIKDNEIFRL
NAATRSYEEI KPEIIRFCFF DELIFKCPPL KALTRYKLVV STYMSASLLN AEGVNRGHFT
HILLDEAGQA SEPENMIAVS NLCLTETVVV LAGDPRQLGP VIYSRDAESL GLGKSYLERL
FECDYYCEGD ENYVTKLVKN YRCHPEILDL PSKLFYDGEL VASKEDTDSV LASLNFLPNK
EFPMVFYGIQ GCDEREGNNP SWFNRIEISK VIETIKRLTA NDCVQEEDIG VITPYRQQVM
KIKEVLDRLD MTEVKVGSVE QFQGQEKQVI IISTVRSTIK HNEFDRAYCL GFLSNPRRFN
VAITRAISLL VIIGNPHIIC KDMNWNKLLW RCVDNNAYQG CGLPEQEEFV EEPFKQEGSS
NGPQYPPEAE WNNSGELNNG GANENGEWSD GWNNNGGTKE KNEWSDGWNS NGGGTKKKDE
WSDGWDNNGG TNGINQEGSS NAPQDPQEAE WNDSGEVKNG GTKEKDVRSD GWNNNGGKNE
KEECCDGWKD GGSGEEIKNG GKFETRGDFV AKEEDEWSDG WK
