6n2v | pdb_00006n2v

Manganese riboswitch from Xanthmonas oryzae bound to Mn(II)

spinqualitylabelsall models 6n2v, resolution 2.85Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6n2v is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MG, MN, NA, SR NonStd Res: GTP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The widespread Mn(2+)-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn(2+) homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 A resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 micros of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg(2+). Only upon adding sub-millimolar Mn(2+), however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn(2+) in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics. Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch.,Suddala KC, Price IR, Dandpat SS, Janecek M, Kuhrova P, Sponer J, Banas P, Ke A, Walter NG Nat Commun. 2019 Sep 20;10(1):4304. doi: 10.1038/s41467-019-12230-5. PMID:31541094 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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