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3adi

From Proteopedia

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Current revision

Structure of Arabidopsis HYL1 and its molecular implications for miRNA processing

Structural highlights

3adi is a 5 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DRB1_ARATH Double-stranded RNA-binding protein involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis by assisting DICER-LIKE 1 (DCL1) in the accurate processing from primary miRNAs (pri-miRNAs) to miRNAs in the nucleus. Forms a complex with SERRATE (SE) and DCL1 to promote accurate processing of pri-miRNAs by DCL1. Binds and assist DCL1 for accurate processing of precursor miRNAs (pre-miRNA). Indirectly involved in the production of trans-acting small interfering RNAs (ta-siRNAs) derived from the TAS1, TAS2 or TAS3 endogenous transcripts by participating in the production of their initiating miRNAs. Involved with argonaute 1 (AGO1) in the guide strand selection from miRNA duplexes, presumably by directional loading of the miRNA duplex (guide stand and passenger strand) onto the RNA-induced silencing complex (RISC) for passenger strand degradation. Does not participate in sense transgene-induced post-transcriptional gene silencing (S-PTGS). Involved in several plant development aspects and response to hormones through its role in miRNAs processing.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Arabidopsis HYPONASTIC LEAVES1 (HYL1) is a double-stranded RNA-binding protein that forms a complex with DICER-LIKE1 (DCL1) and SERRATE to facilitate processing of primary miRNAs into microRNAs (miRNAs). However, the structural mechanisms of miRNA maturation by this complex are poorly understood. Here, we present the crystal structures of double-stranded RNA binding domains (dsRBD1 and dsRBD2) of HYL1 and HYL1 dsRBD1 (HR1)/dsRNA complex as well as human TRBP2 dsRBD2 (TR2)/dsRNA complex for comparison analysis. Structural and functional study demonstrates that both HR1 and TR2 are canonical dsRBDs for dsRNA binding, whereas HR2 of HYL1 is a non-canonical dsRBD harboring a putative dimerization interface. Domain swapping within the context of HYL1 demonstrates that TR2 can supplant the function of HR1 in vitro and in vivo. Further biochemical analyses suggest that HYL1 probably binds to the miRNA/miRNA( *) region of precursors as a dimer mediated by HR2.

Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing.,Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA Structure. 2010 May 12;18(5):594-605. PMID:20462493^[13]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lu C, Fedoroff N. A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell. 2000 Dec;12(12):2351-2366. PMID:11148283
↑ Han MH, Goud S, Song L, Fedoroff N. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):1093-8. Epub 2004 Jan 13. PMID:14722360 doi:http://dx.doi.org/10.1073/pnas.0307969100
↑ Vazquez F, Gasciolli V, Crete P, Vaucheret H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr Biol. 2004 Feb 17;14(4):346-51. PMID:14972688 doi:http://dx.doi.org/10.1016/j.cub.2004.01.035
↑ Hiraguri A, Itoh R, Kondo N, Nomura Y, Aizawa D, Murai Y, Koiwa H, Seki M, Shinozaki K, Fukuhara T. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol Biol. 2005 Jan;57(2):173-88. PMID:15821876 doi:http://dx.doi.org/10.1007/s11103-004-6853-5
↑ Kurihara Y, Takashi Y, Watanabe Y. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA. 2006 Feb;12(2):206-12. PMID:16428603 doi:http://dx.doi.org/10.1261/rna.2146906
↑ Yang L, Liu Z, Lu F, Dong A, Huang H. SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J. 2006 Sep;47(6):841-50. Epub 2006 Aug 2. PMID:16889646 doi:10.1111/j.1365-313X.2006.02835.x
↑ Wu F, Yu L, Cao W, Mao Y, Liu Z, He Y. The N-terminal double-stranded RNA binding domains of Arabidopsis HYPONASTIC LEAVES1 are sufficient for pre-microRNA processing. Plant Cell. 2007 Mar;19(3):914-25. Epub 2007 Mar 2. PMID:17337628 doi:http://dx.doi.org/10.1105/tpc.106.048637
↑ Dong Z, Han MH, Fedoroff N. The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9970-5. doi:, 10.1073/pnas.0803356105. Epub 2008 Jul 16. PMID:18632569 doi:10.1073/pnas.0803356105
↑ Szarzynska B, Sobkowiak L, Pant BD, Balazadeh S, Scheible WR, Mueller-Roeber B, Jarmolowski A, Szweykowska-Kulinska Z. Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs. Nucleic Acids Res. 2009 May;37(9):3083-93. doi: 10.1093/nar/gkp189. Epub 2009 Mar, 20. PMID:19304749 doi:http://dx.doi.org/10.1093/nar/gkp189
↑ Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM. The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA. 2009 Dec;15(12):2219-35. doi: 10.1261/rna.1646909. Epub 2009 Oct 27. PMID:19861421 doi:http://dx.doi.org/10.1261/rna.1646909
↑ Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA. Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure. 2010 May 12;18(5):594-605. PMID:20462493 doi:10.1016/j.str.2010.02.006
↑ Rasia RM, Mateos J, Bologna NG, Burdisso P, Imbert L, Palatnik JF, Boisbouvier J. Structure and RNA interactions of the plant MicroRNA processing-associated protein HYL1. Biochemistry. 2010 Sep 28;49(38):8237-9. PMID:20735118 doi:10.1021/bi100672x
↑ Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA. Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure. 2010 May 12;18(5):594-605. PMID:20462493 doi:10.1016/j.str.2010.02.006

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3adi"

Categories: Arabidopsis thaliana | Large Structures | Chen HY | Yuan YA

@@ Line 3: / Line 3: @@
 <StructureSection load='3adi' size='340' side='right'caption='[[3adi]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3adi]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ADI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ADI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3adi]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ADI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ADI FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3adg|3adg]], [[3adj|3adj]], [[3adl|3adl]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HYL1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3adi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3adi OCA], [https://pdbe.org/3adi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3adi RCSB], [https://www.ebi.ac.uk/pdbsum/3adi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3adi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DRB1_ARATH DRB1_ARATH]] Double-stranded RNA-binding protein involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis by assisting DICER-LIKE 1 (DCL1) in the accurate processing from primary miRNAs (pri-miRNAs) to miRNAs in the nucleus. Forms a complex with SERRATE (SE) and DCL1 to promote accurate processing of pri-miRNAs by DCL1. Binds and assist DCL1 for accurate processing of precursor miRNAs (pre-miRNA). Indirectly involved in the production of trans-acting small interfering RNAs (ta-siRNAs) derived from the TAS1, TAS2 or TAS3 endogenous transcripts by participating in the production of their initiating miRNAs. Involved with argonaute 1 (AGO1) in the guide strand selection from miRNA duplexes, presumably by directional loading of the miRNA duplex (guide stand and passenger strand) onto the RNA-induced silencing complex (RISC) for passenger strand degradation. Does not participate in sense transgene-induced post-transcriptional gene silencing (S-PTGS). Involved in several plant development aspects and response to hormones through its role in miRNAs processing.<ref>PMID:11148283</ref> <ref>PMID:14722360</ref> <ref>PMID:14972688</ref> <ref>PMID:15821876</ref> <ref>PMID:16428603</ref> <ref>PMID:16889646</ref> <ref>PMID:17337628</ref> <ref>PMID:18632569</ref> <ref>PMID:19304749</ref> <ref>PMID:19861421</ref> <ref>PMID:20462493</ref> <ref>PMID:20735118</ref>
+[https://www.uniprot.org/uniprot/DRB1_ARATH DRB1_ARATH] Double-stranded RNA-binding protein involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis by assisting DICER-LIKE 1 (DCL1) in the accurate processing from primary miRNAs (pri-miRNAs) to miRNAs in the nucleus. Forms a complex with SERRATE (SE) and DCL1 to promote accurate processing of pri-miRNAs by DCL1. Binds and assist DCL1 for accurate processing of precursor miRNAs (pre-miRNA). Indirectly involved in the production of trans-acting small interfering RNAs (ta-siRNAs) derived from the TAS1, TAS2 or TAS3 endogenous transcripts by participating in the production of their initiating miRNAs. Involved with argonaute 1 (AGO1) in the guide strand selection from miRNA duplexes, presumably by directional loading of the miRNA duplex (guide stand and passenger strand) onto the RNA-induced silencing complex (RISC) for passenger strand degradation. Does not participate in sense transgene-induced post-transcriptional gene silencing (S-PTGS). Involved in several plant development aspects and response to hormones through its role in miRNAs processing.<ref>PMID:11148283</ref> <ref>PMID:14722360</ref> <ref>PMID:14972688</ref> <ref>PMID:15821876</ref> <ref>PMID:16428603</ref> <ref>PMID:16889646</ref> <ref>PMID:17337628</ref> <ref>PMID:18632569</ref> <ref>PMID:19304749</ref> <ref>PMID:19861421</ref> <ref>PMID:20462493</ref> <ref>PMID:20735118</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Chen, H Y]]
+[[Category: Chen HY]]
-[[Category: Yuan, Y A]]
+[[Category: Yuan YA]]
-[[Category: Gene regulation-rna complex]]
-[[Category: Hyl1]]
-[[Category: Mirna processing mechanism]]
-[[Category: Rna binding protein]]

3adi

From Proteopedia

Current revision

Structure of Arabidopsis HYL1 and its molecular implications for miRNA processing

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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