Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.
Department of Molecular Medicine, University of Pavia, Via Forlanini 3, 27100 Pavia, Italy.
Mol Cell. 2024 Jul 25;84(14):2682-2697.e6. doi: 10.1016/j.molcel.2024.06.016. Epub 2024 Jul 11.
RNA can directly control protein activity in a process called riboregulation; only a few mechanisms of riboregulation have been described in detail, none of which have been characterized on structural grounds. Here, we present a comprehensive structural, functional, and phylogenetic analysis of riboregulation of cytosolic serine hydroxymethyltransferase (SHMT1), the enzyme interconverting serine and glycine in one-carbon metabolism. We have determined the cryoelectron microscopy (cryo-EM) structure of human SHMT1 in its free- and RNA-bound states, and we show that the RNA modulator competes with polyglutamylated folates and acts as an allosteric switch, selectively altering the enzyme's reactivity vs. serine. In addition, we identify the tetrameric assembly and a flap structural motif as key structural elements necessary for binding of RNA to eukaryotic SHMT1. The results presented here suggest that riboregulation may have played a role in evolution of eukaryotic SHMT1 and in compartmentalization of one-carbon metabolism. Our findings provide insights for RNA-based therapeutic strategies targeting this cancer-linked metabolic pathway.
RNA 可以通过一种称为核糖调控的过程直接控制蛋白质活性；尽管已经详细描述了几种核糖调控机制，但没有一种机制是基于结构特征来描述的。在这里，我们对细胞质丝氨酸羟甲基转移酶 1（SHMT1）的核糖调控进行了全面的结构、功能和系统发育分析，该酶在一碳代谢中转化丝氨酸和甘氨酸。我们已经确定了游离态和 RNA 结合态人 SHMT1 的冷冻电镜（cryo-EM）结构，并且我们表明 RNA 调节剂与聚谷氨酸化叶酸竞争，并作为别构开关，选择性地改变酶对丝氨酸的反应性。此外，我们确定了四聚体组装和一个 flap 结构基序作为结合 RNA 到真核 SHMT1 的关键结构元件。这里提出的结果表明，核糖调控可能在真核 SHMT1 的进化和一碳代谢的区室化中发挥了作用。我们的发现为针对这种与癌症相关的代谢途径的基于 RNA 的治疗策略提供了见解。
