CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Nat Microbiol. 2020 Sep;5(9):1107-1118. doi: 10.1038/s41564-020-0731-z. Epub 2020 Jun 1.
Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, endonuclease and translocase activities. Despite extensive studies over the past five decades, little is known about the molecular mechanisms of these sophisticated machines. Here, we report the cryo-electron microscopy structures of the representative EcoR124I R-M system in different assemblies (RMS, RMS and MS) bound to target DNA and the phage and mobile genetic element-encoded anti-restriction proteins Ocr and ArdA. EcoR124I can precisely regulate different enzymatic activities by adopting distinct conformations. The marked conformational transitions of EcoR124I are dependent on the intrinsic flexibility at both the individual-subunit and assembled-complex levels. Moreover, Ocr and ArdA use a DNA-mimicry strategy to inhibit multiple activities, but do not block the conformational transitions of the complexes. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into assembly, operation and inhibition mechanisms of type I R-M systems.
I 型限制修饰（R-M）系统广泛存在于原核基因组中，为其提供了强大的抵御外源 DNA 的保护。它们是多亚基酶，具有甲基转移酶、内切核酸酶和转位酶活性。尽管在过去的五十年中进行了广泛的研究，但对于这些复杂机器的分子机制知之甚少。在这里，我们报告了代表 EcoR124I R-M 系统在不同组装（RMS、RMS 和 MS）与靶 DNA 以及噬菌体和移动遗传元件编码的抗限制蛋白 Ocr 和 ArdA 结合时的冷冻电子显微镜结构。EcoR124I 可以通过采用不同的构象来精确调节不同的酶活性。EcoR124I 的显著构象转变依赖于单个亚基和组装复合物水平的固有灵活性。此外，Ocr 和 ArdA 采用 DNA 模拟策略来抑制多种活性，但不会阻止复合物的构象转变。这些结构发现，辅以关键分子间接触的突变研究，为 I 型 R-M 系统的组装、操作和抑制机制提供了深入了解。
