8F4O

Apo structure of the TPP riboswitch aptamer domain

8F4O の概要

• エントリーDOI: 10.2210/pdb8f4o/pdb
• 分子名称: TPP riboswitch aptamer domain, IRIDIUM HEXAMMINE ION, TRIETHYLENE GLYCOL, ... (4 entities in total)
• 機能のキーワード: rna, riboswitch, aptamer, thiamine pyrophosphate, tpp
• 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: 62335.64

構造登録者

Lee, H.-K.,Wang, Y.-X.,Stagno, J.R. (登録日: 2022-11-11, 公開日: 2023-05-17, 最終更新日: 2023-10-25)

主引用文献

Lee, H.K.,Lee, Y.T.,Fan, L.,Wilt, H.M.,Conrad, C.E.,Yu, P.,Zhang, J.,Shi, G.,Ji, X.,Wang, Y.X.,Stagno, J.R.
Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state.
Structure, 31:848-859.e3, 2023

PubMed Abstract: The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown. Here, we report a 3.1 Å resolution crystal structure of Escherichia coli TPP riboswitch in the apo state, which exhibits an extended, Y-shaped conformation further supported by small-angle X-ray scattering data and driven molecular dynamics simulations. The loss of ligand interactions results in helical uncoiling of P5 and disruption of the key tertiary interaction between the sensory domains. Opening of the aptamer propagates to the gene-regulatory P1 helix and generates the key conformational flexibility needed for the switching behavior. Much of the ligand-binding site at the three-way junction is unaltered, thereby maintaining a partially preformed pocket. Together, these results paint a dynamic picture of the ligand-induced conformational changes in TPP riboswitches that confer conditional gene regulation.

PubMed: 37253356
DOI: 10.1016/j.str.2023.05.003

実験手法

X-RAY DIFFRACTION (3.1 Å)