Ju Jue, Tomita Kozo
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo Kashiwa, Chiba, Japan.
Nat Commun. 2025 Aug 21;16(1):7708. doi: 10.1038/s41467-025-63021-0.
The N-methyladenosine (mA) modification in U6 snRNA, catalyzed by METTL16 using S-adenosylmethionine (SAM) as the methyl donor, is required for efficient and accurate pre-mRNA splicing. However, the mechanism by which METTL16 modifies U6 snRNA with mA remains elusive. Here, we present cryo-EM structures of METTL16 in complex with U6 snRNA, providing insights into the METTL16-mediated modification of U6 snRNA with mA. The structures reveal that U6 snRNA is recruited to METTL16 through specific interactions between the C-terminal kinase-associated 1 (KA-1) domain of METTL16 and the internal stem-loop (ISL) of U6 snRNA. Upon SAM binding to the catalytic pocket within the N-terminal methyltransferase domain (MTD), U6 snRNA undergoes a structural rearrangement that positions the target adenine-containing motif at the catalytic site. This conformational change is followed by an additional structural adjustment of U6 snRNA into a productive conformation, bringing the target adenosine closer to SAM within the catalytic pocket and thereby ensuring efficient mA modification. The KA-1 domain functions as a scaffold for initial substrate recognition and facilitates the subsequent dynamic methylation process within the MTD, highlighting the cooperative roles of METTL16 domains for U6 snRNA modification.
由METTL16以S-腺苷甲硫氨酸（SAM）作为甲基供体催化的U6小核RNA（snRNA）中的N-甲基腺苷（mA）修饰，是高效准确的前体mRNA剪接所必需的。然而，METTL16用mA修饰U6 snRNA的机制仍然不清楚。在这里，我们展示了METTL16与U6 snRNA复合物的冷冻电镜结构，为METTL16介导的U6 snRNA的mA修饰提供了见解。这些结构表明，U6 snRNA通过METTL16的C端激酶相关1（KA-1）结构域与U6 snRNA的内部茎环（ISL）之间的特异性相互作用被招募到METTL16。当SAM结合到N端甲基转移酶结构域（MTD）内的催化口袋时，U6 snRNA发生结构重排，将含目标腺嘌呤的基序定位在催化位点。这种构象变化之后是U6 snRNA进一步的结构调整，进入一个有效的构象，使目标腺苷在催化口袋内更靠近SAM，从而确保有效的mA修饰。KA-1结构域作为初始底物识别的支架，并促进MTD内随后的动态甲基化过程，突出了METTL16结构域在U6 snRNA修饰中的协同作用。
