4Y1M

An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state

4Y1M の概要

• エントリーDOI: 10.2210/pdb4y1m/pdb
• 関連するPDBエントリー: 4Y1I 4Y1J
• 分子名称: E. coli yybP-ykoY riboswitch, STRONTIUM ION, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: riboswitch, manganese, free state, rna
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 76135.56

構造登録者

Price, I.R.,Ke, A. (登録日: 2015-02-08, 公開日: 2015-04-08, 最終更新日: 2024-02-28)

主引用文献

Price, I.R.,Gaballa, A.,Ding, F.,Helmann, J.D.,Ke, A.
Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.
Mol.Cell, 57:1110-1123, 2015

PubMed Abstract: Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a ∼30-40 μM affinity for Mn(2+). We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.

PubMed: 25794619
DOI: 10.1016/j.molcel.2015.02.016

実験手法

X-RAY DIFFRACTION (3 Å)