Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch
Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch
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DOI：
10.1073/pnas.1111701108
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发表时间：
2011-09-06
影响因子：
11.1
通讯作者：
Serganov, Alexander
中科院分区：
文献类型：
--
作者：
Huang, Lili;Ishibe-Murakami, Satoko;Serganov, Alexander
四氢叶酸（THF）是维生素叶酸（B9）的一种生物活性形式，是一碳转移反应中的重要辅因子。在细菌中，叶酸相关基因的表达是通过响应THF和相关化合物与核糖开关的特异性结合的反馈调节来控制的。在这里，我们提出了在配体结合和未结合状态下的真杆菌核糖开关的THF传感结构域的X射线结构。该结构揭示了一个“倒置”的三路交界处的架构，最不寻常的核糖开关，与交界处位于远离监管螺旋P1和不直接参与螺旋P1的形成。相反，通过与配体结合而稳定的三向连接使核糖开关茎对齐，用于长距离三级假结相互作用，其有助于螺旋P1的组织，因此规定了核糖开关的调节反应。配体的蝶呤部分停靠在连接点附近的半开放口袋中，在那里它与两个适度保守的嘧啶形成特异性氢键。氨基苯甲酸部分堆叠在鸟嘌呤碱基上，而谷氨酸部分似乎不与RNA发生强烈的相互作用。与其他核糖开关相比，这些发现表明THF核糖开关使用有限数量的可用决定簇用于配体识别。鉴于现代抗生素靶向叶酸代谢，THF核糖开关结构提供了核糖开关功能的机制方面的见解，并可能有助于操纵病原菌中的THF水平。
Tetrahydrofolate (THF), a biologically active form of the vitamin folate (B9), is an essential cofactor in one-carbon transfer reactions. In bacteria, expression of folate-related genes is controlled by feedback modulation in response to specific binding of THF and related compounds to a riboswitch. Here, we present the X-ray structures of the THF-sensing domain from the Eubacterium siraeum riboswitch in the ligand-bound and unbound states. The structure reveals an "inverted" three-way junctional architecture, most unusual for riboswitches, with the junction located far from the regulatory helix P1 and not directly participating in helix P1 formation. Instead, the three-way junction, stabilized by binding to the ligand, aligns the riboswitch stems for long-range tertiary pseudoknot interactions that contribute to the organization of helix P1 and therefore stipulate the regulatory response of the riboswitch. The pterin moiety of the ligand docks in a semiopen pocket adjacent to the junction, where it forms specific hydrogen bonds with two moderately conserved pyrimidines. The aminobenzoate moiety stacks on a guanine base, whereas the glutamate moiety does not appear to make strong interactions with the RNA. In contrast to other riboswitches, these findings demonstrate that the THF riboswitch uses a limited number of available determinants for ligand recognition. Given that modern antibiotics target folate metabolism, the THF riboswitch structure provides insights on mechanistic aspects of riboswitch function and may help in manipulating THF levels in pathogenic bacteria.