6cb3 | pdb_00006cb3

Crystal structure of the L.Lactis YkoY riboswitch bound to cadmium

spinqualitylabelsall models 6cb3, resolution 1.89Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6cb3 is a 2 chain structure with sequence from Lactococcus lactis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.891Å Ligands: BA, CD, GTP, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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