Gu Yajie, Li Huan, Deep Amar, Enustun Eray, Zhang Dapeng, Corbett Kevin D
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Department of Biology, Saint Louis University, Saint Louis, MO, USA.
Mol Cell. 2025 Feb 6;85(3):523-536.e6. doi: 10.1016/j.molcel.2024.12.004. Epub 2024 Dec 31.
Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease. Here, we reveal the structural basis for activation of Bacillus cereus Shedu. Two cryoelectron microscopy structures of Shedu show that it switches between inactive and active states through conformational changes affecting active-site architecture, which are controlled by the protein's N-terminal domain (NTD). We find that B. cereus Shedu cleaves near DNA ends with a 3' single-stranded overhang, likely enabling it to specifically degrade the DNA injected by certain bacteriophages. Bioinformatic analysis of Shedu homologs reveals a conserved nuclease domain with remarkably diverse N-terminal regulatory domains: we identify 79 distinct NTD types falling into eight broad classes, including those with predicted nucleic acid binding, enzymatic, and other activities. Together, these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs that likely respond to a range of signals.
原核生物拥有多种抗噬菌体免疫系统，包括单蛋白Shedu核酸酶。在此，我们揭示了蜡样芽孢杆菌Shedu激活的结构基础。Shedu的两个冷冻电子显微镜结构表明，它通过影响活性位点结构的构象变化在无活性状态和活性状态之间切换，这些变化由蛋白质的N端结构域（NTD）控制。我们发现蜡样芽孢杆菌Shedu在具有3'单链突出端的DNA末端附近切割，这可能使其能够特异性降解某些噬菌体注入的DNA。对Shedu同源物的生物信息学分析揭示了一个保守的核酸酶结构域，其N端调节结构域具有显著的多样性：我们确定了79种不同的NTD类型，分为八大类，包括具有预测的核酸结合、酶活性和其他活性的类型。总之，这些数据揭示Shedu是一类广泛的免疫核酸酶家族，具有由多种NTD调节的共同核酸酶核心，这些NTD可能对一系列信号作出反应。
