6cb3: Difference between revisions
New page: '''Unreleased structure''' The entry 6cb3 is ON HOLD Authors: Description: Category: Unreleased Structures |
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The | ==Crystal structure of the L.Lactis YkoY riboswitch bound to cadmium== | ||
<StructureSection load='6cb3' size='340' side='right'caption='[[6cb3]], [[Resolution|resolution]] 1.89Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6cb3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CB3 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]] 1.891Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=6cb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cb3 OCA], [https://pdbe.org/6cb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cb3 RCSB], [https://www.ebi.ac.uk/pdbsum/6cb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cb3 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn(2+). X-ray crystallography revealed a binuclear cation-binding pocket. This comprises one hexacoordinate site, with six oxygen ligands, which preorganizes the second, with five oxygen and one nitrogen ligands. The relatively soft nitrogen ligand was proposed to confer affinity for Mn(2+), but how this excludes other soft cations remained enigmatic. By subjecting representative yybP-ykoY riboswitches to diverse cations in vitro, we now find that these RNAs exhibit limited transition metal ion selectivity. Among the cations tested, Cd(2+) and Mn(2+) bind most tightly, and comparison of three new Cd(2+)-bound crystal structures suggests that these riboswitches achieve selectivity by enforcing heptacoordination (favored by high-spin Cd(2+) and Mn(2+), but otherwise uncommon) in the softer site. Remarkably, the Cd(2+)- and Mn(2+)-selective bacterial transcription factor MntR also uses heptacoordination within a binuclear site to achieve selectivity. | |||
Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.,Bachas ST, Ferre-D'Amare AR Cell Chem Biol. 2018 May 4. pii: S2451-9456(18)30146-6. doi:, 10.1016/j.chembiol.2018.04.016. PMID:29805037<ref>PMID:29805037</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6cb3" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Lactococcus lactis]] | |||
[[Category: Large Structures]] | |||
[[Category: Bachas S]] | |||
[[Category: Ferre-D'amare AR]] | |||
Latest revision as of 18:00, 4 October 2023
Crystal structure of the L.Lactis YkoY riboswitch bound to cadmiumCrystal structure of the L.Lactis YkoY riboswitch bound to cadmium
Structural highlights
Publication Abstract from PubMedThe large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn(2+). X-ray crystallography revealed a binuclear cation-binding pocket. This comprises one hexacoordinate site, with six oxygen ligands, which preorganizes the second, with five oxygen and one nitrogen ligands. The relatively soft nitrogen ligand was proposed to confer affinity for Mn(2+), but how this excludes other soft cations remained enigmatic. By subjecting representative yybP-ykoY riboswitches to diverse cations in vitro, we now find that these RNAs exhibit limited transition metal ion selectivity. Among the cations tested, Cd(2+) and Mn(2+) bind most tightly, and comparison of three new Cd(2+)-bound crystal structures suggests that these riboswitches achieve selectivity by enforcing heptacoordination (favored by high-spin Cd(2+) and Mn(2+), but otherwise uncommon) in the softer site. Remarkably, the Cd(2+)- and Mn(2+)-selective bacterial transcription factor MntR also uses heptacoordination within a binuclear site to achieve selectivity. Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.,Bachas ST, Ferre-D'Amare AR Cell Chem Biol. 2018 May 4. pii: S2451-9456(18)30146-6. doi:, 10.1016/j.chembiol.2018.04.016. PMID:29805037[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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