Q8GYD9 (SDE3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Probable RNA helicase SDE3
EC=3.6.4.13

Alternative name(s):
Silencing defective protein 3

Gene names

Name:	SDE3
Ordered Locus Names:	At1g05460
ORF Names:	T25N20.11, T25N20.26

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	1002 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Probable RNA helicase required for post-transcriptional gene silencing (PTGS), a process that provides protection in plants against virus infection and can suppress expression of transgenes. Plays a central role in RNA interference (RNAi) process, a process that mediates mRNA destruction of translational repression. Required for the assembly of the RISC complex, a complex required for target RNA destruction or repression. May be required in the RISC assembly to unwind miRNAs, in the production of single-stranded miRNA from the double-stranded miRNA, a key step in RISC formation. Involved in the amplification of sense-PTGS (S-PTGS), leading to siRNA production. Required for the maintenance but not the initiation of tobacco rattle virus (TRV)-mediated silencing, probably by mediating/maintaining DNA methylation and chromatin-based transcriptional gene silencing at some genomic locations. Ref.1 Ref.5 Ref.6 Ref.7
Catalytic activity	ATP + H2O = ADP + phosphate.
Subunit structure	Interacts with AGO1 and AGO2. Ref.7
Subcellular location	Cytoplasm Probable.
Disruption phenotype	Delayed loss of transgene silencing (post-transcriptional gene silencing (PTGS)), with full silencing in the cotyledons and in the hypocotyl, contrasting with a loss of silencing in true leaves. Impaired maintenance of tobacco rattle virus (TRV)-mediated silencing. Reduced methylation of cytosine residues in targets loci but enrichment of histone-H3 'Lys-4' methylation (H3K4me3) at the same sites. Ref.5 Ref.7
Sequence similarities	Belongs to the DNA2/NAM7 helicase family. SDE3 subfamily.
Sequence caution	The sequence AAF79736.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	RNA-mediated gene silencing
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	posttranscriptional gene silencing by RNA Inferred from mutant phenotype Ref.7. Source: UniProtKB virus induced gene silencing Inferred from mutant phenotype Ref.1. Source: TAIR
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA helicase activity Inferred from sequence or structural similarity Ref.1. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1002	1002	Probable RNA helicase SDE3		PRO_0000080709
Regions
	Nucleotide binding	421 – 428	8	ATP Potential
	Region	871 – 1001	131	GW-rich, involved in binding to AGO proteins
	Motif	545 – 548	4	DEAG box
Experimental info
	Mutagenesis	427	1	K → A: Loss of helicase activity. Ref.7
	Mutagenesis	888	1	W → F: Loss of binding to AGO1 and AGO4. Ref.7
	Sequence conflict	329	1	M → L in AAK40099. Ref.1
	Sequence conflict	535	1	N → K in AAK40099. Ref.1
	Sequence conflict	646	1	D → E in AAK40099. Ref.1
	Sequence conflict	991	1	A → G in AAK40099. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q8GYD9 [UniParc]. Last modified March 1, 2003. Version 1. Checksum: 32D906F7FA95C0A5	FASTA	1,002	113,363
	10 20 30 40 50 60 MSVSGYKSDD EYSVIADKGE IGFIDYQNDG SSGCYNPFDE GPVVVSVPFP FKKEKPQSVT 70 80 90 100 110 120 VGETSFDSFT VKNTMDEPVD LWTKIYASNP EDSFTLSILK PPSKDSDLKE RQCFYETFTL 130 140 150 160 170 180 EDRMLEPGDT LTIWVSCKPK DIGLHTTVVT VDWGSDRVER VVFLLAEDKI SSSLTSNRPY 190 200 210 220 230 240 SRSRRAPKKD FAVDDYVKGS RPSKVVERSF RNRLPLYEIP KEIREMIENK EFPDDLNEGL 250 260 270 280 290 300 TARNYANYYK TLLIMEELQL EEDMRAYDME NVSMKRRGIY LSLEVPGLAE RRPSLVHGDF 310 320 330 340 350 360 IFVRHAYDDG TDHAYQGFVH RVEADEVHMK FASEFHQRHT AGSVYNVRFT YNRINTRRLY 370 380 390 400 410 420 QAVDAAEMLD PNFLFPSLHS GKRMIKTKPF VPISPALNAE QICSIEMVLG CKGAPPYVIH 430 440 450 460 470 480 GPPGTGKTMT LVEAIVQLYT TQRNARVLVC APSNSAADHI LEKLLCLEGV RIKDNEIFRL 490 500 510 520 530 540 NAATRSYEEI KPEIIRFCFF DELIFKCPPL KALTRYKLVV STYMSASLLN AEGVNRGHFT 550 560 570 580 590 600 HILLDEAGQA SEPENMIAVS NLCLTETVVV LAGDPRQLGP VIYSRDAESL GLGKSYLERL 610 620 630 640 650 660 FECDYYCEGD ENYVTKLVKN YRCHPEILDL PSKLFYDGEL VASKEDTDSV LASLNFLPNK 670 680 690 700 710 720 EFPMVFYGIQ GCDEREGNNP SWFNRIEISK VIETIKRLTA NDCVQEEDIG VITPYRQQVM 730 740 750 760 770 780 KIKEVLDRLD MTEVKVGSVE QFQGQEKQVI IISTVRSTIK HNEFDRAYCL GFLSNPRRFN 790 800 810 820 830 840 VAITRAISLL VIIGNPHIIC KDMNWNKLLW RCVDNNAYQG CGLPEQEEFV EEPFKQEGSS 850 860 870 880 890 900 NGPQYPPEAE WNNSGELNNG GANENGEWSD GWNNNGGTKE KNEWSDGWNS NGGGTKKKDE 910 920 930 940 950 960 WSDGWDNNGG TNGINQEGSS NAPQDPQEAE WNDSGEVKNG GTKEKDVRSD GWNNNGGKNE 970 980 990 1000 KEECCDGWKD GGSGEEIKNG GKFETRGDFV AKEEDEWSDG WK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis." Dalmay T., Horsefield R., Braunstein T.H., Baulcombe D.C. EMBO J. 20:2069-2078(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Functional annotation of a full-length Arabidopsis cDNA collection." Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K. Science 296:141-145(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Unravelling PTGS: SDE3 - an RNA helicase involved in RNA silencing in Arabidopsis." Willmann M.R. Trends Plant Sci. 6:344-345(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[6]	"Transitivity-dependent and -independent cell-to-cell movement of RNA silencing." Himber C., Dunoyer P., Moissiard G., Ritzenthaler C., Voinnet O. EMBO J. 22:4523-4533(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions." Garcia D., Garcia S., Pontier D., Marchais A., Renou J.P., Lagrange T., Voinnet O. Mol. Cell 48:109-120(2012) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT, INTERACTION WITH AGO1 AND AGO4, MUTAGENESIS OF LYS-427 AND TRP-888, DISRUPTION PHENOTYPE. Strain: cv. Columbia.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF339908 Genomic DNA. Translation: AAK40099.1. AC005106 Genomic DNA. Translation: AAF79736.1. Sequence problems. CP002684 Genomic DNA. Translation: AEE27843.1. AK117698 mRNA. Translation: BAC42350.1.
IPI	IPI00521883.
PIR	C86189.
RefSeq	NP_172037.1. NM_100425.3.
UniGene	At.15329. At.42398.
3D structure databases
ProteinModelPortal	Q8GYD9.
SMR	Q8GYD9. Positions 391-834.
ModBase	Search...
Proteomic databases
PaxDb	Q8GYD9.
PRIDE	Q8GYD9.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G05460.1; AT1G05460.1; AT1G05460.
GeneID	837047.
KEGG	ath:AT1G05460.
Organism-specific databases
GeneFarm	2423. 136.
TAIR	At1g05460.
Phylogenomic databases
eggNOG	COG1112.
HOGENOM	HOG000239755.
InParanoid	Q8GYD9.
OMA	DEREGNN.
PhylomeDB	Q8GYD9.
ProtClustDB	CLSN2682016.
Gene expression databases
Genevestigator	Q8GYD9.
GermOnline	AT1G05460. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR027417. P-loop_NTPase. IPR026127. SDE3. [Graphical view]
PANTHER	PTHR10887:SF165. PTHR10887:SF165. 1 hit.
SUPFAM	SSF52540. SSF52540. 1 hit.
ProtoNet	Search...

Entry information

Entry name

SDE3_ARATH

Accession

Primary (citable) accession number: Q8GYD9
Secondary accession number(s): Q94KS1, Q9LR48

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	March 1, 2003
Last modified:	May 29, 2013
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program