View source for 6vuh


==APO PreQ1 riboswitch aptamer grown in Mn2+==
<StructureSection load='6vuh' size='340' side='right'caption='[[6vuh]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6vuh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VUH FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.999&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6vuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vuh OCA], [https://pdbe.org/6vuh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vuh RCSB], [https://www.ebi.ac.uk/pdbsum/6vuh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vuh ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 A and 2.65 A-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1-exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1-sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.,Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE Nucleic Acids Res. 2020 Aug 20;48(14):8146-8164. doi: 10.1093/nar/gkaa546. PMID:32597951<ref>PMID:32597951</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 6vuh" style="background-color:#fffaf0;"></div>

==See Also==
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
[[Category: Large Structures]]
[[Category: Jenkins JL]]
[[Category: Wedekind JE]]