6N2V
Manganese riboswitch from Xanthmonas oryzae bound to Mn(II)
Summary for 6N2V
| Entry DOI | 10.2210/pdb6n2v/pdb |
| Descriptor | X. oryzae Mn riboswitch optimized construct, MAGNESIUM ION, MANGANESE (II) ION, ... (6 entities in total) |
| Functional Keywords | riboswitch, rna, manganese |
| Biological source | Xanthomonas oryzae |
| Total number of polymer chains | 2 |
| Total formula weight | 66706.29 |
| Authors | Price, I.R.,Ke, A. (deposition date: 2018-11-14, release date: 2019-10-02, Last modification date: 2023-10-11) |
| Primary citation | Suddala, K.C.,Price, I.R.,Dandpat, S.S.,Janecek, M.,Kuhrova, P.,Sponer, J.,Banas, P.,Ke, A.,Walter, N.G. Local-to-global signal transduction at the core of a Mn2+sensing riboswitch. Nat Commun, 10:4304-4304, 2019 Cited by PubMed Abstract: The widespread Mn-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 µs 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. Only upon adding sub-millimolar Mn, however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn 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. PubMed: 31541094DOI: 10.1038/s41467-019-12230-5 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.85 Å) |
Structure validation
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