Recently, a novel two-gene bacterial defense system against phages, encoding a SIR2 NADase and a HerA ATPase/helicase, has been identified. However, the molecular mechanism of the bacterial SIR2–HerA immune system remains unclear. Here, we determine the cryo-EM structures of SIR2, HerA and their complex from Paenibacillus sp. 453MF in different functional states. The SIR2 proteins oligomerize into a dodecameric ring-shaped structure consisting of two layers of interlocked hexamers, in which each subunit exhibits an auto-inhibited conformation. Distinct from the canonical AAA+ proteins, HerA hexamer alone in this antiphage system adopts a split spiral arrangement, which is stabilized by a unique C-terminal extension. SIR2 and HerA proteins assemble into a ∼1.1 MDa torch-shaped complex to fight against phage infection. Importantly, disruption of the interactions between SIR2 and HerA largely abolishes the antiphage activity. Interestingly, binding alters the oligomer state of SIR2, switching from a dodecamer to a tetradecamer state. The formation of the SIR2–HerA binary complex activates NADase and nuclease activities in SIR2 and ATPase and helicase activities in HerA. Together, our study not only provides a structural basis for the functional communications between SIR2 and HerA proteins, but also unravels a novel concerted antiviral mechanism through NAD+ degradation, ATP hydrolysis, and DNA cleavage.

中文翻译：

---

SIR2-HerA 系统中协同抗噬菌体活性的结构基础


最近，已经确定了一种针对噬菌体的新型双基因细菌防御系统，编码 SIR2 NADase 和 HerA ATP 酶/解旋酶。然而，细菌 SIR2-HerA 免疫系统的分子机制仍不清楚。在这里，我们确定了来自不同功能状态的 Paenibacillus sp. 453MF 的 SIR2、HerA 及其复合物的冷冻电镜结构。SIR2 蛋白寡聚化成十二聚体环状结构，由两层互锁的六聚体组成，其中每个亚基都表现出自抑制构象。与经典的 AAA+ 蛋白不同，该抗噬菌体系统中单独的 HerA 六聚体采用分裂螺旋排列，通过独特的 C 端延伸来稳定。SIR2 和 HerA 蛋白组装成 ∼1.1 MDa 火炬状复合物，以对抗噬菌体感染。重要的是，SIR2 和 HerA 之间相互作用的破坏在很大程度上消除了抗噬细胞活性。有趣的是，结合会改变 SIR2 的寡聚体状态，从十二聚体状态转变为十四聚体状态。SIR2-HerA 二元复合物的形成激活 SIR2 和 ATP 酶中的 NADase 和核酸酶活性，以及 HerA 中的解旋酶活性。总之，我们的研究不仅为 SIR2 和 HerA 蛋白之间的功能通讯提供了结构基础，而且还通过 NAD+ 降解、ATP 水解和 DNA 切割揭示了一种新的协同抗病毒机制。