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==Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak== | ==Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak== | ||
<StructureSection load='7elp' size='340' side='right'caption='[[7elp]]' scene=''> | <StructureSection load='7elp' size='340' side='right'caption='[[7elp]], [[Resolution|resolution]] 2.79Å' 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=7ELP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELP FirstGlance]. <br> | <table><tr><td colspan='2'>[[7elp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ELP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELP 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=7elp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7elp OCA], [https://pdbe.org/7elp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7elp RCSB], [https://www.ebi.ac.uk/pdbsum/7elp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7elp ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=IR:IRIDIUM+ION'>IR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XAN:XANTHINE'>XAN</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=7elp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7elp OCA], [https://pdbe.org/7elp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7elp RCSB], [https://www.ebi.ac.uk/pdbsum/7elp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7elp ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch. | |||
Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.,Xu X, Egger M, Chen H, Bartosik K, Micura R, Ren A Nucleic Acids Res. 2021 Jun 14. pii: 6298625. doi: 10.1093/nar/gkab486. PMID:34125892<ref>PMID:34125892</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7elp" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ren | [[Category: Ren, A M]] | ||
[[Category: Xu | [[Category: Xu, X C]] | ||
[[Category: Riboswitch]] | |||
[[Category: Rna]] | |||
[[Category: Xanthine]] | |||
Revision as of 12:14, 21 July 2021
Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soakCrystal structure of xanthine riboswitch with xanthine, iridium hexammine soak
Structural highlights
Publication Abstract from PubMedRiboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch. Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.,Xu X, Egger M, Chen H, Bartosik K, Micura R, Ren A Nucleic Acids Res. 2021 Jun 14. pii: 6298625. doi: 10.1093/nar/gkab486. PMID:34125892[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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