Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA
Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA
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DOI：
10.1261/rna.060954.117
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发表时间：
2017-07-01
期刊：
影响因子：
4.5
通讯作者：
Nielsen, Klaus H.
中科院分区：
文献类型：
--
作者：
He, Yangzi;Staley, Jonathan P.;Nielsen, Klaus H.
核酸依赖性ATP酶的三个家族（DEAH/RHA、Skit样和NS 3/NPH-II），称为DExH ATP酶，被认为通过沿着单链核酸的进行性ATP依赖性3'至5'易位来执行无数功能。虽然病毒NS 3/NPH-II家族的易位机制已被广泛研究，但尚不清楚该家族出现的原理是否或如何扩展到其他两个家族。在这里，我们报告的晶体结构的酵母DEAH/RHA家族ATP酶Prp 43 p，其功能在剪接和核糖体生物合成，在复杂的聚尿嘧啶和不可水解的ATP类似物。该结构揭示了在催化核心的RecAl结构域内基序Ib的保守的DEAH/RHA特异性变异，其中基序延长为夹在中央RNA堆叠的3'端的β-发夹，这是在病毒和Ski-2家族中由辅助结构域执行的功能。支持易位的基本作用，在这个发夹突变废除解旋酶活性，而不影响RNA结合或ATP酶活性。虽然该结构揭示了与RecA 1结构域中的病毒ATP酶的差异，但我们的结构证明了与催化核心的RecA 2结构域中的病毒ATP酶的惊人相似性，包括在RNA堆叠的5'端的突出的β-发夹和涉及介导易位的动态基序Va。我们的晶体结构，遗传和生物化学实验，以及与其他DExH ATP酶的比较，支持一个通用的机制，DExH类解旋酶涉及一对书挡，沿沿着RNA蠕动。
Three families of nucleic acid-dependent ATPases (DEAH/RHA, Skit-like, and NS3/NPH-II), termed the DExH ATPases, are thought to execute myriad functions by processive, ATP-dependent, 3' to 5' translocation along single-stranded nucleic acid. While the mechanism of translocation of the viral NS3/NPH-II family has been studied extensively, it has not been clear if or how the principles that have emerged for this family extend to the other two families. Here we report the crystal structure of the yeast DEAH/RHA family ATPase Prp43p, which functions in splicing and ribosome biogenesis, in complex with poly-uracil and a nonhydrolyzable ATP analog. The structure reveals a conserved DEAH/RHA-specific variation of motif lb within the RecA1 domain of the catalytic core, in which the motif elongates as a beta-hairpin that bookends the 3' end of a central RNA stack, a function that in the viral and Ski-2 families is performed by an auxiliary domain. Supporting a fundamental role in translocation, mutations in this hairpin abolished helicase activity without affecting RNA binding or ATPase activity. While the structure reveals differences with viral ATPases in the RecA1 domain, our structure demonstrates striking similarities with viral ATPases in the RecA2 domain of the catalytic core, including both a prominent beta-hairpin that bookends the 5' end of the RNA stack and a dynamic motif Va that is implicated in mediating translocation. Our crystal structure, genetic, and biochemical experiments, as well as comparisons with other DExH ATPases, support a generalized mechanism for the DExH class of helicases involving a pair of bookends that inchworm along RNA.