4FEJ

Crystal structure of the A24U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine

4FEJ の概要

• エントリーDOI: 10.2210/pdb4fej/pdb
• 関連するPDBエントリー: 1U8D 4FE5 4FEL 4FEN 4FEO 4FEP
• 分子名称: A24U mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain, HYPOXANTHINE, ACETATE ION, ... (5 entities in total)
• 機能のキーワード: three-way junction with distal tertiary interaction, genetic regulatory element, hypoxanthine, rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 22865.76

構造登録者

Stoddard, C.D.,Trausch, J.J.,Widmann, J.,Marcano, J.,Knight, R.,Batey, R.T. (登録日: 2012-05-30, 公開日: 2013-02-27, 最終更新日: 2024-02-28)

主引用文献

Stoddard, C.D.,Widmann, J.,Trausch, J.J.,Marcano-Velazquez, J.G.,Knight, R.,Batey, R.T.
Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch.
J.Mol.Biol., 425:1596-1611, 2013

PubMed Abstract: Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs.

PubMed: 23485418
DOI: 10.1016/j.jmb.2013.02.023

実験手法

X-RAY DIFFRACTION (1.5 Å)