Department of Biochemistry, University of California, Riverside, CA 92521, USA.
Nucleic Acids Res. 2020 Jun 19;48(11):6326-6339. doi: 10.1093/nar/gkaa324.
Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures of XPB in complex with Bax1 from Archaeoglobus fulgidus (Af) and Sulfolobus tokodaii (St). These structures reveal for the first time four domains in Bax1, which interacts with XPB mainly through its N-terminal domain. A Cas2-like domain likely helps to position Bax1 at the forked DNA allowing the nuclease domain to incise one arm of the fork. Bax1 exists in monomer or homodimer but forms a heterodimer exclusively with XPB. StBax1 keeps StXPB in a closed conformation and stimulates ATP hydrolysis by XPB while AfBax1 maintains AfXPB in the open conformation and reduces its ATPase activity. Bax1 contains two distinguished nuclease active sites to presumably incise DNA damage. Our results demonstrate that protein-protein interactions regulate the activities of XPB ATPase and Bax1 nuclease. These structures provide a platform to understand the XPB-nuclease interactions important for the coordination of DNA unwinding and damage incision in eukaryotic NER.
核苷酸切除修复（NER）是多种 DNA 损伤的主要 DNA 修复途径。XPB 在损伤部位的 DNA 打开和协调核酸内切酶的损伤切割中起关键作用。XPB 从古菌到人都是保守的。在古菌中，XPB 与核酸内切酶 Bax1 相关。在这里，我们报告了 XPB 与来自古生球菌属（Af）和硫矿硫化叶菌（St）的 Bax1 复合物的晶体结构。这些结构首次揭示了 Bax1 中的四个结构域，它主要通过其 N 端结构域与 XPB 相互作用。一个 Cas2 样结构域可能有助于将 Bax1 定位在分叉 DNA 上，从而使核酸内切酶结构域能够切割叉的一条臂。Bax1 以单体或同源二聚体形式存在，但仅与 XPB 形成异源二聚体。StBax1 使 StXPB 保持在封闭构象并刺激 XPB 的 ATP 水解，而 AfBax1 使 AfXPB 保持在开放构象并降低其 ATP 酶活性。Bax1 包含两个有区别的核酸内切酶活性位点，大概用于切割 DNA 损伤。我们的结果表明，蛋白质-蛋白质相互作用调节 XPB ATP 酶和 Bax1 核酸内切酶的活性。这些结构为理解 XPB-核酸内切酶相互作用提供了一个平台，该相互作用对于真核 NER 中 DNA 解旋和损伤切割的协调很重要。
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