Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.
Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA.
Nucleic Acids Res. 2020 Nov 18;48(20):11721-11736. doi: 10.1093/nar/gkaa866.
The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.
尾噬菌体和疱疹病毒的基因组包装马达是由几个大（TerL）和小（TerS）端酶亚基组成的强大纳米机器。该马达在空的前体衣壳（或原衣壳）的门顶点处短暂组装，以实现基因组包裹。端酶亚基已经进行了深入研究，尤其是在感染大肠杆菌或沙门氏菌的经典噬菌体中，但对具有越来越多生物医学相关性的假单胞菌噬菌体的包装马达了解较少。在这里，我们研究了感染铜绿假单胞菌的三种 Podoviridae 噬菌体的小端酶亚基。我们发现 TerS 在溶液中是多态的，但在其高亲和力肝素结合构象中组装成非九聚体。假单胞菌噬菌体 PaP3 TerS 的原子结构，这是第一个完整的 cos 噬菌体的 TerS 结构，揭示了九个螺旋-转角-螺旋（HTH）基序围绕着一个β-链通道不对称排列，这个通道太窄而无法容纳 DNA。PaP3 TerS 在体外以序列特异性的方式结合 DNA。X 射线散射和分子建模表明，TerS 在溶液中采用开放构象，其特征是动态 HTH 围绕寡聚化核心移动，为 DNA 生成离散的结合缝隙。我们提出了一种模型，用于通过 DNA 的侧向交错来特异性识别包装起始位点。
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