4KQY

Bacillus subtilis yitJ S box/SAM-I riboswitch

「3NPB」から置き換えられました

4KQY の概要

• エントリーDOI: 10.2210/pdb4kqy/pdb
• 分子名称: YitJ S box/SAM-I riboswitch, S-ADENOSYLMETHIONINE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: gene regulation, rna
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 39019.19

構造登録者

Lu, C. (登録日: 2013-05-15, 公開日: 2013-08-07, 最終更新日: 2024-03-20)

主引用文献

Lu, C.,Ding, F.,Chowdhury, A.,Pradhan, V.,Tomsic, J.,Holmes, W.M.,Henkin, T.M.,Ke, A.
SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch
J.Mol.Biol., 404:803-818, 2010

PubMed Abstract: S-box (SAM-I) riboswitches are a widespread class of riboswitches involved in the regulation of sulfur metabolism in Gram-positive bacteria. We report here the 3.0-Å crystal structure of the aptamer domain of the Bacillus subtilis yitJ S-box (SAM-I) riboswitch bound to S-adenosyl-L-methionine (SAM). The RNA folds into two sets of helical stacks spatially arranged by tertiary interactions including a K-turn and a pseudoknot at a four-way junction. The tertiary structure is further stabilized by metal coordination, extensive ribose zipper interactions, and SAM-mediated tertiary interactions. Despite structural differences in the peripheral regions, the SAM-binding core of the B. subtilis yitJ riboswitch is virtually superimposable with the previously determined Thermoanaerobacter tengcongensis yitJ riboswitch structure, suggesting that a highly conserved ligand-recognition mechanism is utilized by all S-box riboswitches. SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemical probing analysis further revealed that the alternative base-pairing element in the expression platform controls the conformational switching process. In the absence of SAM, the apo yitJ aptamer domain folds predominantly into a pre-binding conformation that resembles, but is not identical with, the SAM-bound state. We propose that SAM enters the ligand-binding site through the "J1/2-J3/4" gate and "locks" down the SAM-bound conformation through an induced-fit mechanism. Temperature-dependent SHAPE revealed that the tertiary interaction-stabilized SAM-binding core is extremely stable, likely due to the cooperative RNA folding behavior. Mutational studies revealed that certain modifications in the SAM-binding region result in loss of SAM binding and constitutive termination, which suggests that these mutations lock the RNA into a form that resembles the SAM-bound form in the absence of SAM.

PubMed: 20951706
DOI: 10.1016/j.jmb.2010.09.059

実験手法

X-RAY DIFFRACTION (3.02 Å)