2l2n: Difference between revisions

Revision as of 08:09, 25 July 2018

Backbone 1H, 13C, and 15N Chemical Shift Assignments for the first dsRBD of protein HYL1

Structural highlights

2l2n is a 1 chain structure with sequence from Arath. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2l2m
Gene:	At1g09700, F21M12.9 (ARATH)
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

HYL1 is a double-stranded RNA binding protein involved in microRNA processing in plants. HYL1 enhances the efficiency and precision of the RNase III protein DCL1 and participates in microRNA strand selection. In this work, we dissect the contributions of the domains of HYL1 to the binding of RNA targets. We found that the first domain is the main contributor to RNA binding. Mapping of the interaction regions by nuclear magnetic resonance on the structure of HYL1 RNA-binding domains showed that the difference in binding capabilities can be traced to sequence divergence in beta2-beta3 loop. The possible role of each domain is discussed in light of previous experimental data.

Structure and RNA interactions of the plant MicroRNA processing-associated protein HYL1.,Rasia RM, Mateos J, Bologna NG, Burdisso P, Imbert L, Palatnik JF, Boisbouvier J Biochemistry. 2010 Sep 28;49(38):8237-9. PMID:20735118^[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:https://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:https://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:https://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:https://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:https://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:https://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:https://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
↑ 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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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:https://dx.doi.org/10.1073/pnas.0307969100

[3] 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:https://dx.doi.org/10.1016/j.cub.2004.01.035

[4] 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:https://dx.doi.org/10.1007/s11103-004-6853-5

[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:https://dx.doi.org/10.1261/rna.2146906

[6] 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

[7] 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:https://dx.doi.org/10.1105/tpc.106.048637

[8] 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

[9] 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:https://dx.doi.org/10.1093/nar/gkp189

[10] 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:https://dx.doi.org/10.1261/rna.1646909

[11] 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

[12] 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

[13] 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

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@@ Line 1: / Line 1: @@
 ==Backbone 1H, 13C, and 15N Chemical Shift Assignments for the first dsRBD of protein HYL1==
 <StructureSection load='2l2n' size='340' side='right' caption='[[2l2n]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2l2m|2l2m]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g09700, F21M12.9 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l2n OCA], [http://pdbe.org/2l2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l2n RCSB], [http://www.ebi.ac.uk/pdbsum/2l2n PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l2n OCA], [http://pdbe.org/2l2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l2n RCSB], [http://www.ebi.ac.uk/pdbsum/2l2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l2n ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l2/2l2n_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l2/2l2n_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2l2n ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

2l2n: Difference between revisions

Revision as of 08:09, 25 July 2018

Backbone 1H, 13C, and 15N Chemical Shift Assignments for the first dsRBD of protein HYL1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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