5DDP

L-glutamine riboswitch bound with L-glutamine

5DDP の概要

• エントリーDOI: 10.2210/pdb5ddp/pdb
• 関連するPDBエントリー: 5DDO 5DDQ 5DDR
• 分子名称: RNA (61-MER), U1 small nuclear ribonucleoprotein A, GLUTAMINE, ... (6 entities in total)
• 機能のキーワード: riboswitch, l-glutamine, bound-form, rna, rna binding protein-rna complex, rna binding protein/rna
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 62640.82

構造登録者

Ren, A.,Patel, D.J. (登録日: 2015-08-25, 公開日: 2015-12-23, 最終更新日: 2024-03-06)

主引用文献

Ren, A.,Xue, Y.,Peselis, A.,Serganov, A.,Al-Hashimi, H.M.,Patel, D.J.
Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.
Cell Rep, 13:1800-1813, 2015

PubMed Abstract: Naturally occurring L-glutamine riboswitches occur in cyanobacteria and marine metagenomes, where they reside upstream of genes involved in nitrogen metabolism. By combining X-ray, NMR, and MD, we characterized an L-glutamine-dependent conformational transition in the Synechococcus elongatus glutamine riboswitch from tuning fork to L-shaped alignment of stem segments. This transition generates an open ligand-binding pocket with L-glutamine selectivity enforced by Mg(2+)-mediated intermolecular interactions. The transition also stabilizes the P1 helix through a long-range "linchpin" Watson-Crick G-C pair-capping interaction, while melting a short helix below P1 potentially capable of modulating downstream readout. NMR data establish that the ligand-free glutamine riboswitch in Mg(2+) solution exists in a slow equilibrium between flexible tuning fork and a minor conformation, similar, but not identical, to the L-shaped bound conformation. We propose that an open ligand-binding pocket combined with a high conformational penalty for forming the ligand-bound state provide mechanisms for reducing binding affinity while retaining high selectivity.

PubMed: 26655897
DOI: 10.1016/j.celrep.2015.10.062

実験手法

X-RAY DIFFRACTION (2.302 Å)