SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch.
SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch.
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DOI：
10.1016/j.jmb.2010.09.059
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发表时间：
2010-12-17
影响因子：
5.6
通讯作者：
Ke A
中科院分区：
文献类型：
--
作者：
Lu C;Ding F;Chowdhury A;Pradhan V;Tomsic J;Holmes WM;Henkin TM;Ke A
S-box（SAM-I）核糖开关是一类广泛存在的核糖开关，参与革兰氏阳性菌硫代谢的调控。本文报道了枯草芽孢杆菌yitJ S-box（SAM-I）核糖开关与S-腺苷-L-甲硫氨酸（SAM）结合的适体结构域的3.0-ε晶体结构。RNA折叠成两套螺旋堆叠空间排列的三级相互作用，包括一个K-转弯和一个假结在一个四路交界处。三级结构通过金属配位、广泛的核糖拉链相互作用和SAM介导的三级相互作用进一步稳定。尽管在外围区域存在结构差异，但B.枯草杆菌yitJ核糖开关与先前确定的腾冲嗜热厌氧杆菌yitJ核糖开关结构几乎是重叠的，这表明高度保守的配体识别机制被所有的S盒核糖开关利用。SHAPE（selective 2′-hydroxyacylation analyzed by primer extension）化学探针分析进一步揭示了表达平台中的替代碱基配对元件控制构象转换过程。在不存在SAM的情况下，apo yit 1适体结构域主要折叠成类似于但不与SAM结合状态相同的结合前构象。我们提出SAM通过“J1/2-J3/4”门进入配体结合位点，并通过诱导配合机制“锁定”SAM结合构象。温度依赖性SHAPE显示，三级相互作用稳定的SAM结合核心非常稳定，可能是由于合作RNA折叠行为。突变研究表明，SAM结合区的某些修饰导致SAM结合的丧失和组成性终止，这表明这些突变将RNA锁定为与SAM结合形式相似的形式。
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.
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DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
14.9
作者：
Huang W;Kim J;Jha S;Aboul-ela F
通讯作者：
Aboul-ela F
影响因子：
5.4
作者：
Dambach, Michael D.;Winkler, Wade C.
通讯作者：
Winkler, Wade C.
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
代谢物结合核糖开关的分布，机制和结构。
影响因子：
12.3
作者：
Barrick, Jeffrey E;Breaker, Ronald R
通讯作者：
Breaker, Ronald R