Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand.
Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand.
Biochemistry. 2024 Jun 4;63(11):1493-1504. doi: 10.1021/acs.biochem.4c00161. Epub 2024 May 14.
DNA gyrases catalyze negative supercoiling of DNA, are essential for bacterial DNA replication, transcription, and recombination, and are important antibacterial targets in multiple pathogens, including , which in 2021 caused >1.5 million deaths worldwide. DNA gyrase is a tetrameric (AB) protein formed from two subunit types: gyrase A (GyrA) carries the breakage-reunion active site, whereas gyrase B (GyrB) catalyzes ATP hydrolysis required for energy transduction and DNA translocation. The GyrB ATPase domains dimerize in the presence of ATP to trap the translocated DNA (T-DNA) segment as a first step in strand passage, for which hydrolysis of one of the two ATPs and release of the resulting inorganic phosphate is rate-limiting. Here, dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations of the dimeric 43 kDa N-terminal fragment of GyrB show how events at the ATPase site (dissociation/hydrolysis of bound nucleotides) are propagated through communication pathways to other functionally important regions of the GyrB ATPase domain. Specifically, our simulations identify two distinct pathways that respectively connect the GyrB ATPase site to the corynebacteria-specific C-loop, thought to interact with GyrA prior to DNA capture, and to the C-terminus of the GyrB transduction domain, which in turn contacts the C-terminal GyrB topoisomerase-primase (TOPRIM) domain responsible for interactions with GyrA and the centrally bound G-segment DNA. The connection between the ATPase site and the C-loop of dimeric GyrB is consistent with the unusual properties of DNA gyrase relative to those from other bacterial species.
DNA 回旋酶催化 DNA 的负超螺旋化，是细菌 DNA 复制、转录和重组所必需的，并且是包括在内的多种病原体中的重要抗菌靶标，该病原体在 2021 年导致全球超过 150 万人死亡。DNA 回旋酶是由两种亚基类型组成的四聚体（AB）蛋白：gyrase A（GyrA）携带断裂-重连活性位点，而 gyrase B（GyrB）催化用于能量转导和 DNA 易位的 ATP 水解。在 ATP 的存在下，GyrB 的 ATP 酶结构域二聚化以捕获作为链通过第一步的易位 DNA（T-DNA）片段，其中两个 ATP 之一的水解和产生的无机磷酸盐的释放是限速步骤。在这里，GyrB 的 43 kDa N 端片段的双分子动态非平衡分子动力学（D-NEMD）模拟显示了 ATP 酶位点（结合核苷酸的解离/水解）的事件如何通过通讯途径传播到 GyrB ATP 酶结构域的其他功能重要区域。具体来说，我们的模拟确定了两条不同的途径，它们分别将 GyrB ATP 酶位点连接到推测在 DNA 捕获之前与 GyrA 相互作用的棒状杆菌特异性 C 环，以及 GyrB 易位结构域的 C 末端，该结构域反过来与负责与 GyrA 和中央结合的 G 段 DNA 相互作用的 GyrB 拓扑异构酶-引物（TOPRIM）结构域的 C 末端接触。二聚体 GyrB 中的 ATP 酶位点和 C 环之间的连接与 DNA 回旋酶相对于其他细菌物种的异常特性一致。
