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==The second dsRBD domain from A. thaliana DICER-LIKE 1==
==The second dsRBD domain from A. thaliana DICER-LIKE 1==
<StructureSection load='2lrs' size='340' side='right'caption='[[2lrs]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
<StructureSection load='2lrs' size='340' side='right'caption='[[2lrs]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2lrs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LRS FirstGlance]. <br>
<table><tr><td colspan='2'>[[2lrs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LRS FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DCL1, ASU1, CAF SIN1, SUS1, At1g01040, T25K16.4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2lrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrs OCA], [https://pdbe.org/2lrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lrs RCSB], [https://www.ebi.ac.uk/pdbsum/2lrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrs ProSAT]</span></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=2lrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrs OCA], [https://pdbe.org/2lrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lrs RCSB], [https://www.ebi.ac.uk/pdbsum/2lrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrs ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DCL1_ARATH DCL1_ARATH]] Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Functions with DRB1/HYL1 and SERRATE proteins for accurate pri-miRNAs to miRNAs processing. 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 in the processing of natural siRNAs (nat-siRNAs, derived from cis-natural antisense transcripts) by cleaving 24 nucleotide nat-siRNAs into 21 nucleotide nat-siRNAs. Can produce RDR6-dependent endogenous ta-siRNAs derived from TAS1 and TAS2. Required for the production of 30-40 nucleotide bacterial-induced long siRNAs (lsiRNA). Acts redundantly with DICER-LIKE 3 (DCL3) to promote flowering via repression of FLOWERING LOCUS C (FLC). Represses antiviral RNA silencing through negative regulation of the expression of DCL4 and DCL3.<ref>PMID:15821876</ref> <ref>PMID:16040244</ref> <ref>PMID:16428603</ref> <ref>PMID:17579240</ref> <ref>PMID:18003861</ref> <ref>PMID:18632569</ref> <ref>PMID:18799732</ref> 
[https://www.uniprot.org/uniprot/DCL1_ARATH DCL1_ARATH] Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Functions with DRB1/HYL1 and SERRATE proteins for accurate pri-miRNAs to miRNAs processing. 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 in the processing of natural siRNAs (nat-siRNAs, derived from cis-natural antisense transcripts) by cleaving 24 nucleotide nat-siRNAs into 21 nucleotide nat-siRNAs. Can produce RDR6-dependent endogenous ta-siRNAs derived from TAS1 and TAS2. Required for the production of 30-40 nucleotide bacterial-induced long siRNAs (lsiRNA). Acts redundantly with DICER-LIKE 3 (DCL3) to promote flowering via repression of FLOWERING LOCUS C (FLC). Represses antiviral RNA silencing through negative regulation of the expression of DCL4 and DCL3.<ref>PMID:15821876</ref> <ref>PMID:16040244</ref> <ref>PMID:16428603</ref> <ref>PMID:17579240</ref> <ref>PMID:18003861</ref> <ref>PMID:18632569</ref> <ref>PMID:18799732</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Dicer-like ribonuclease III enzymes are involved in different paths related to RNA silencing in plants. Little is known about the structural aspects of these processes. Here we present a structural characterization of the second double-stranded RNA binding domain (dsRBD) of DCL1, which is presumed to participate in pri-micro-RNA recognition and subcellular localization of this protein. We determined the solution structure and found that it has a canonical fold but bears some variation with respect to other homologous domains. We also found that this domain binds both double-stranded RNA and double-stranded DNA, in contrast to most dsRBDs. Our characterization shows that this domain likely has functions other than substrate recognition and binding.
 
Second Double-Stranded RNA Binding Domain of Dicer-like Ribonuclease 1: Structural and Biochemical Characterization.,Burdisso P, Suarez IP, Bologna NG, Palatnik JF, Bersch B, Rasia RM Biochemistry. 2012 Dec 21;51(51):10159-66. doi: 10.1021/bi301247r. Epub 2012 Dec , 12. PMID:23194006<ref>PMID:23194006</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2lrs" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arath]]
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bersch, B]]
[[Category: Bersch B]]
[[Category: Boisbouvier, J]]
[[Category: Boisbouvier J]]
[[Category: Bologna, N]]
[[Category: Bologna N]]
[[Category: Burdisso, P]]
[[Category: Burdisso P]]
[[Category: Palatnik, J]]
[[Category: Palatnik J]]
[[Category: Rasia, R]]
[[Category: Rasia R]]
[[Category: Suarez, I]]
[[Category: Suarez I]]
[[Category: Hydrolase]]
[[Category: Mirna]]
[[Category: Rna binding]]

Latest revision as of 09:57, 1 May 2024

The second dsRBD domain from A. thaliana DICER-LIKE 1The second dsRBD domain from A. thaliana DICER-LIKE 1

Structural highlights

2lrs is a 1 chain structure with sequence from Arabidopsis thaliana. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DCL1_ARATH Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Functions with DRB1/HYL1 and SERRATE proteins for accurate pri-miRNAs to miRNAs processing. 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 in the processing of natural siRNAs (nat-siRNAs, derived from cis-natural antisense transcripts) by cleaving 24 nucleotide nat-siRNAs into 21 nucleotide nat-siRNAs. Can produce RDR6-dependent endogenous ta-siRNAs derived from TAS1 and TAS2. Required for the production of 30-40 nucleotide bacterial-induced long siRNAs (lsiRNA). Acts redundantly with DICER-LIKE 3 (DCL3) to promote flowering via repression of FLOWERING LOCUS C (FLC). Represses antiviral RNA silencing through negative regulation of the expression of DCL4 and DCL3.[1] [2] [3] [4] [5] [6] [7]

References

  1. ↑ 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
  2. ↑ Gasciolli V, Mallory AC, Bartel DP, Vaucheret H. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol. 2005 Aug 23;15(16):1494-500. PMID:16040244 doi:http://dx.doi.org/S0960-9822(05)00765-7
  3. ↑ 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
  4. ↑ Schmitz RJ, Hong L, Fitzpatrick KE, Amasino RM. DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana. Genetics. 2007 Jun;176(2):1359-62. PMID:17579240 doi:http://dx.doi.org/10.1534/genetics.107.070649
  5. ↑ Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H. A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev. 2007 Dec 1;21(23):3123-34. Epub 2007 Nov 14. PMID:18003861 doi:http://dx.doi.org/10.1101/gad.1595107
  6. ↑ 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
  7. ↑ Qu F, Ye X, Morris TJ. Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14732-7. doi:, 10.1073/pnas.0805760105. Epub 2008 Sep 17. PMID:18799732 doi:http://dx.doi.org/10.1073/pnas.0805760105
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