7elr: Difference between revisions
New page: '''Unreleased structure''' The entry 7elr is ON HOLD Authors: Description: Category: Unreleased Structures |
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The | ==Crystal structure of xanthine riboswitch with xanthine== | ||
<StructureSection load='7elr' size='340' side='right'caption='[[7elr]], [[Resolution|resolution]] 2.66Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7elr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ideonella_sp._B508-1 Ideonella sp. B508-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ELR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELR 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]] 2.66Å</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=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=7elr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7elr OCA], [https://pdbe.org/7elr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7elr RCSB], [https://www.ebi.ac.uk/pdbsum/7elr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7elr ProSAT]</span></td></tr> | |||
</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> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 7elr" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Ideonella sp. B508-1]] | |||
[[Category: Large Structures]] | |||
[[Category: Ren AM]] | |||
[[Category: Xu XC]] | |||
Latest revision as of 19:56, 29 November 2023
Crystal structure of xanthine riboswitch with xanthineCrystal structure of xanthine riboswitch with xanthine
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. See AlsoReferences
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