Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Nucleic Acids Res. 2024 Sep 23;52(17):10705-10716. doi: 10.1093/nar/gkae717.
Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.
RNA 的加工是所有生命系统的关键调控机制。大肠杆菌蛋白 YicC 属于高度保守的 YicC 家族，被鉴定为一种新型的核糖核酸酶。在这里，我们报道了大肠杆菌 YicC 脱辅基蛋白的 2.8 Å 分辨率晶体结构和与 RNA 底物结合的 YicC 的 3.2 Å 冷冻电镜结构。脱辅基 YicC 形成三聚体二聚体，具有大的开放通道。在 RNA 结合形式中，YicC 的顶部三聚体旋转近 70°，并将 RNA 底物封闭在腔体内，形成蛤壳-珍珠构象，与其他已知的核糖核酸酶都不同。结构信息结合质谱和生化数据确定了在 RNA 发夹的上游进行切割。突变研究表明，以前未表征的结构域 DUF1732 在 RNA 结合和催化中都很关键。这些研究揭示了以前未探索的 YicC 核糖核酸酶家族的机制。
