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==Burkholderia sp. TJI49 Guanidine-I riboswitch== | ==Burkholderia sp. TJI49 Guanidine-I riboswitch== | ||
<StructureSection load='7mlw' size='340' side='right'caption='[[7mlw]]' scene=''> | <StructureSection load='7mlw' size='340' side='right'caption='[[7mlw]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MLW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MLW FirstGlance]. <br> | <table><tr><td colspan='2'>[[7mlw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_sp._TJI49 Burkholderia sp. TJI49]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MLW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MLW FirstGlance]. <br> | ||
</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=7mlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mlw OCA], [https://pdbe.org/7mlw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mlw RCSB], [https://www.ebi.ac.uk/pdbsum/7mlw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mlw ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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=7mlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mlw OCA], [https://pdbe.org/7mlw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mlw RCSB], [https://www.ebi.ac.uk/pdbsum/7mlw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mlw ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The widespread ykkC-I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the Burkholderia sp. TJI49 ykkC-I subtype-1 (Guanidine-I) riboswitch aptamer domain. Differing from the previously reported structures of orthologs from Dickeya dadantii and Sulfobacillus acidophilus, our Burkholderia structure reveals a chelated K(+) ion adjacent to two Mg(2+) ions in the guanidine-binding pocket. Thermal melting analysis shows that K(+) chelation, which induces localized conformational changes in the binding pocket, improves guanidinium-RNA interactions. Analysis of ribosome structures suggests that the [K(+)(Mg(2+))2] ion triad is uncommon. It is, however, reminiscent of metal ion clusters found in the active sites of ribozymes and DNA polymerases. Previous structural characterization of ykkC-I subtype-2 RNAs, which bind the effector ligands ppGpp and PRPP, indicate that in those paralogs, an adenine responsible for K(+) chelation in the Burkholderia Guanidine-I riboswitch is replaced by a pyrimidine. This mutation results in a water molecule and Mg(2+) ion binding in place of the K(+) ion. Thus, our structural analysis demonstrates how ion and solvent chelation tune divergent ligand specificity and affinity among ykkC-I riboswitches. | |||
An uncommon [K(+)(Mg(2+))2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch.,Trachman RJ 3rd, Ferre-D'Amare AR RNA. 2021 Oct;27(10):1257-1264. doi: 10.1261/rna.078824.121. Epub 2021 Jul 13. PMID:34257148<ref>PMID:34257148</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7mlw" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Burkholderia sp. TJI49]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ferre-D'Amare AR]] | [[Category: Ferre-D'Amare AR]] | ||
[[Category: Trachman RJ]] | [[Category: Trachman RJ]] | ||