6N2V

Manganese riboswitch from Xanthmonas oryzae bound to Mn(II)

6N2V の概要

• エントリーDOI: 10.2210/pdb6n2v/pdb
• 分子名称: X. oryzae Mn riboswitch optimized construct, MAGNESIUM ION, MANGANESE (II) ION, ... (6 entities in total)
• 機能のキーワード: riboswitch, rna, manganese
• 由来する生物種: Xanthomonas oryzae
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 66706.29

構造登録者

Price, I.R.,Ke, A. (登録日: 2018-11-14, 公開日: 2019-10-02, 最終更新日: 2023-10-11)

主引用文献

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

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: 31541094
DOI: 10.1038/s41467-019-12230-5
主引用文献が同じPDBエントリー

実験手法

X-RAY DIFFRACTION (2.85 Å)