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==NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement==
==NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement==
<StructureSection load='2mtk' size='340' side='right'caption='[[2mtk]], [[NMR_Ensembles_of_Models | 21 NMR models]]' scene=''>
<StructureSection load='2mtk' size='340' side='right'caption='[[2mtk]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2mtk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MTK FirstGlance]. <br>
<table><tr><td colspan='2'>[[2mtk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MTK FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2mtj|2mtj]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=2mtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mtk OCA], [https://pdbe.org/2mtk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mtk RCSB], [https://www.ebi.ac.uk/pdbsum/2mtk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mtk 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=2mtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mtk OCA], [https://pdbe.org/2mtk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mtk RCSB], [https://www.ebi.ac.uk/pdbsum/2mtk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mtk ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The VS ribozyme is a catalytic RNA found within some natural isolates of Neurospora that is being used as a model system to improve our understanding of RNA structure, catalysis, and engineering. The catalytic domain contains five helical domains (SLII-SLVI) that are organized by two three-way junctions. The III-IV-V junction is required for high-affinity binding of the substrate domain (SLI) through formation of a kissing loop interaction with SLV. Here, we determine the high-resolution nuclear magnetic resonance (NMR) structure of a 47-nucleotide RNA containing the III-IV-V junction (J345). The J345 RNA adopts a Y-shaped fold typical of the family C three-way junctions, with coaxial stacking between stems III and IV and an acute angle between stems III and V. The NMR structure reveals that the core of the III-IV-V junction contains four stacked base triples, a U-turn motif, a cross-strand stacking interaction, an A-minor interaction, and a ribose zipper. In addition, the NMR structure shows that the cCUUGg tetraloop used to stabilize stem IV adopts a novel RNA tetraloop fold, different from the known gCUUGc tetraloop structure. Using Mn(2+)-induced paramagnetic relaxation enhancement, we identify six Mg(2+)-binding sites within J345, including one associated with the cCUUGg tetraloop and two with the junction core. The NMR structure of J345 likely represents the conformation of the III-IV-V junction in the context of the active VS ribozyme and suggests that this junction functions as a dynamic hinge that contributes to substrate recognition and catalysis. Moreover, this study highlights a new role for family C three-way junctions in long-range tertiary interactions.


Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement.,Bonneau E, Legault P Biochemistry. 2014 Oct 7;53(39):6264-75. doi: 10.1021/bi500826n. Epub 2014 Sep, 19. PMID:25238589<ref>PMID:25238589</ref>
==See Also==
 
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2mtk" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bonneau, E]]
[[Category: Neurospora crassa]]
[[Category: Legault, P]]
[[Category: Bonneau E]]
[[Category: Base triple]]
[[Category: Legault P]]
[[Category: Cuug tetraloop]]
[[Category: Gaaa tetraloop]]
[[Category: Ribose zipper]]
[[Category: Rna]]
[[Category: Three-way junction]]
[[Category: U-turn]]
[[Category: Vs ribozyme]]

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