View source for 9ljn


==Crystal structure of Guanine-II riboswitch in complex with guanine==
<StructureSection load='9ljn' size='340' side='right'caption='[[9ljn]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9ljn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Unclassified_Paenibacillus Unclassified Paenibacillus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9LJN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9LJN 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]] 2.75&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GUN:GUANINE'>GUN</scene>, <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=9ljn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ljn OCA], [https://pdbe.org/9ljn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ljn RCSB], [https://www.ebi.ac.uk/pdbsum/9ljn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ljn ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A comprehensive understanding of the fundamental principles governing RNA-small molecule interactions is crucial for advancing RNA-targeting therapeutics with small molecules. Riboswitches, a class of noncoding RNAs, regulate gene expression by direct interaction with small-molecule metabolites. In this work, we report an in-depth structure-based investigation of a newly identified riboswitch, Guanine-II, which, despite sharing a conserved scaffold with the Guanine-I riboswitch, exhibits strikingly distinct small molecule ligand-binding characteristics. Through a comprehensive structural analysis of the Guanine-II riboswitch bound to various guanine analogs, combined with comparative studies of other guanine riboswitch variants, including Guanine-I and Xanthine-II riboswitches, as well as isothermal titration calorimetry, we reveal local structural rearrangements that precisely modulate small-molecule ligand adaptability. We further demonstrate that subtle differences in the composition and peripheral architecture of the binding pocket are key determinants of ligand-binding specificity. Additionally, based on the similarity in ligand recognition patterns with the tetrahydrofolate-II riboswitch, we identified additional compounds that bind to the Guanine-II riboswitch through a structure-guided rational search, providing valuable structural insights for the discovery of small molecules targeting RNA.

Ligand specificity and adaptability revealed by the first Guanine-II riboswitch tertiary structure.,Li H, Shen X, Xu X, Tai X, He M, Zhang J, Ren A Nucleic Acids Res. 2025 Sep 5;53(17):gkaf884. doi: 10.1093/nar/gkaf884. PMID:40966503<ref>PMID:40966503</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9ljn" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Unclassified Paenibacillus]]
[[Category: Li HC]]
[[Category: Ren AM]]