Bundit Kamsri, Pharit Kamsri, Auradee Punkvang, Aunlika Chimprasit, Patchreenart Saparpakorn, Supa Hannongbua, James Spencer, A. Sofia F. Oliveira*, Adrian J. Mulholland* and Pornpan Pungpo*,
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引用次数: 0
Abstract
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 Mycobacterium tuberculosis, which in 2021 caused >1.5 million deaths worldwide. DNA gyrase is a tetrameric (A2B2) 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 M. tuberculosis 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 M. tuberculosis DNA gyrase relative to those from other bacterial species.
DNA 回旋酶催化 DNA 的负超螺旋,对细菌的 DNA 复制、转录和重组至关重要,是包括结核分枝杆菌在内的多种病原体的重要抗菌靶标。DNA 回旋酶是一种四聚体(A2B2)蛋白质,由两种亚基类型组成:回旋酶 A(GyrA)携带断裂重组活性位点,而回旋酶 B(GyrB)催化能量转移和 DNA 易位所需的 ATP 水解。GyrB ATP 酶结构域在 ATP 存在时会二聚化,以捕获转位的 DNA(T-DNA)片段,这是链传导的第一步,其中两个 ATP 之一的水解以及由此产生的无机磷酸的释放是限速过程。在这里,对结核杆菌 GyrB 的 43 kDa N 端二聚体片段进行的动态非平衡分子动力学(D-NEMD)模拟显示了 ATPase 位点的事件(结合核苷酸的解离/水解)是如何通过通信途径传播到 GyrB ATPase 结构域的其他重要功能区的。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 ATPase 位点与被认为在捕获 DNA 之前与 GyrA 相互作用的棒状杆菌特异性 C 环连接起来,以及与 GyrB 转导结构域的 C 端连接起来,后者又与负责与 GyrA 和中心结合的 G 段 DNA 相互作用的 C 端 GyrB 拓扑异构酶-primase(TOPRIM)结构域连接起来。ATPase 位点与二聚体 GyrB 的 C 环之间的联系与结核杆菌 DNA 回旋酶相对于其他细菌物种的不寻常特性是一致的。
期刊介绍:
Biochemistry provides an international forum for publishing exceptional, rigorous, high-impact research across all of biological chemistry. This broad scope includes studies on the chemical, physical, mechanistic, and/or structural basis of biological or cell function, and encompasses the fields of chemical biology, synthetic biology, disease biology, cell biology, nucleic acid biology, neuroscience, structural biology, and biophysics. In addition to traditional Research Articles, Biochemistry also publishes Communications, Viewpoints, and Perspectives, as well as From the Bench articles that report new methods of particular interest to the biological chemistry community.