Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany.
Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.
Nucleic Acids Res. 2021 May 21;49(9):5369-5381. doi: 10.1093/nar/gkab316.
The CCCH-type zinc finger (ZnF) containing ZC3H12 ribonucleases are crucial in post-transcriptional immune homoeostasis with ZC3H12A being the only structurally studied member of the family. In this study, we present a structural-biochemical characterization of ZC3H12C, which is linked with chronic immune disorders like psoriasis. We established that the RNA substrate is cooperatively recognized by the PIN and ZnF domains of ZC3H12C and analyzed the crystal structure of ZC3H12C bound to a single-stranded RNA substrate. The RNA engages in hydrogen-bonded contacts and stacking interactions with the PIN and ZnF domains simultaneously. The ZC3H12 ZnF shows unprecedented structural features not previously observed in any member of the CCCH-ZnF family and utilizes stacking interactions via a unique combination of spatially conserved aromatic residues to align the target transcript in a bent conformation onto the ZnF scaffold. Further comparative structural analysis of ZC3H12 CCCH-ZnF suggests that a trinucleotide sequence is recognized by ZC3H12 ZnF in target RNA. Our work not only describes the initial structure-biochemical study on ZC3H12C, but also provides the first molecular insight into RNA recognition by a ZC3H12 family member. Finally, our work points to an evolutionary code for RNA recognition adopted by CCCH-type ZnF proteins.
CCCH 型锌指 (ZnF) 结构域包含的 ZC3H12 核糖核酸酶在转录后免疫稳态中起着至关重要的作用，其中 ZC3H12A 是该家族中唯一进行结构研究的成员。在这项研究中，我们对 ZC3H12C 进行了结构生化特性的研究，因为它与银屑病等慢性免疫紊乱有关。我们确定了 RNA 底物是由 ZC3H12C 的 PIN 和 ZnF 结构域协同识别的，并分析了 ZC3H12C 与单链 RNA 底物结合的晶体结构。该 RNA 与 PIN 和 ZnF 结构域同时发生氢键和堆积相互作用。ZC3H12 ZnF 具有前所未有的结构特征，在 CCCH-ZnF 家族的任何成员中都没有观察到，并且利用空间保守的芳香族残基的独特组合进行堆叠相互作用，将靶转录物以弯曲构象排列在 ZnF 支架上。对 ZC3H12 CCCH-ZnF 的进一步比较结构分析表明，三核苷酸序列被 ZC3H12 ZnF 在靶 RNA 中识别。我们的工作不仅描述了对 ZC3H12C 的初步结构生化研究，而且还首次提供了对 ZC3H12 家族成员识别 RNA 的分子见解。最后，我们的工作指出了 CCCH 型 ZnF 蛋白采用的 RNA 识别进化密码。
