MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China.
MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
Cell. 2022 Nov 10;185(23):4347-4360.e17. doi: 10.1016/j.cell.2022.09.037. Epub 2022 Oct 4.
Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.
病毒 RNA 帽子结构的装饰在 SARS-CoV-2 的增殖中起着至关重要的作用。在这里，我们报告了一种 SARS-CoV-2 RNA 加帽的机制，并记录了原子分辨率的结构细节。聚合酶中的 NiRAN 结构域催化 RNA 5' 端与 nsp9 的第一个残基的共价连接（称为 RNAylation），从而与 GTP 再次由 NiRAN 催化形成帽核（GpppA）。我们还揭示了三磷酸核苷酸类似物抑制剂可以与 nsp9 结合，并适合 NiRAN 中一个以前未知的“Nuc-pocket”，从而抑制 nsp9 RNAylation 和 GpppA 的形成。NiRAN 中的 S-环（50-KTN-52 残基）呈现出与索非布韦单磷酸盐结合的 RTC 中观察到的显著构象变化，这表明存在一种“诱导-锁定”机制来设计抑制剂。这些发现不仅提高了对 SARS-CoV-2 RNA 加帽和 NAI 作用模式的理解，而且为设计抗病毒药物提供了一种策略。
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