6DLQ

PRPP Riboswitch bound to PRPP, manganese chloride soaked structure

6DLQ の概要

• エントリーDOI: 10.2210/pdb6dlq/pdb
• 分子名称: PRPP Riboswitch, 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose, MANGANESE (II) ION, ... (6 entities in total)
• 機能のキーワード: riboswitch, non-coding, rna, ykkc
• 由来する生物種: Syntrophothermus lipocalidus DSM 12680
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36082.89

構造登録者

Peselis, A.,Serganov, A. (登録日: 2018-06-02, 公開日: 2018-11-14, 最終更新日: 2024-03-13)

主引用文献

Peselis, A.,Serganov, A.
ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.
Nat. Chem. Biol., 14:887-894, 2018

PubMed Abstract: The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg-mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution.

PubMed: 30120360
DOI: 10.1038/s41589-018-0114-4

実験手法

X-RAY DIFFRACTION (2.8 Å)