Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan.
Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.
Nucleic Acids Res. 2019 Feb 28;47(4):2113-2129. doi: 10.1093/nar/gky1251.
ParABS, an important DNA partitioning process in chromosome segregation, includes ParA (an ATPase), ParB (a parS binding protein) and parS (a centromere-like DNA). The homologous proteins of ParA and ParB in Helicobacter pylori are HpSoj and HpSpo0J, respectively. We analyzed the ATPase activity of HpSoj and found that it is enhanced by both DNA and HpSpo0J. Crystal structures of HpSoj and its DNA complexes revealed a typical ATPase fold and that it is dimeric. DNA binding by HpSoj is promoted by ATP. The HpSoj-ATP-DNA complex non-specifically binds DNA through a continuous basic binding patch formed by lysine residues, with a single DNA-binding site. This complex exhibits a DNA-binding adept state with an active ATP-bound conformation, whereas the HpSoj-ADP-DNA complex may represent a transient DNA-bound state. Based on structural comparisons, HpSoj exhibits a similar DNA binding surface to the bacterial ParA superfamily, but the archaeal ParA superfamily exhibits distinct non-specific DNA-binding via two DNA-binding sites. We detected the HpSpo0J-HpSoj-DNA complex by electron microscopy and show that this nucleoid-adaptor complex (NAC) is formed through HpSoj and HpSpo0J interaction and parS DNA binding. NAC formation is promoted by HpSoj participation and specific parS DNA facilitation.
ParABS 是染色体分离过程中的一种重要 DNA 分区过程，包括 ParA（一种 ATP 酶）、ParB（一个 parS 结合蛋白）和 parS（一个类似着丝粒的 DNA）。幽门螺杆菌中 ParA 和 ParB 的同源蛋白分别是 HpSoj 和 HpSpo0J。我们分析了 HpSoj 的 ATP 酶活性，发现它同时被 DNA 和 HpSpo0J 增强。HpSoj 及其 DNA 复合物的晶体结构揭示了一个典型的 ATP 酶折叠结构，它是二聚体。DNA 结合由 ATP 促进。HpSoj 通过由赖氨酸残基形成的连续碱性结合点非特异性地结合 DNA，具有一个单一的 DNA 结合位点。该复合物表现出具有活性 ATP 结合构象的 DNA 结合适应状态，而 HpSoj-ADP-DNA 复合物可能代表一个瞬时 DNA 结合状态。基于结构比较，HpSoj 表现出与细菌 ParA 超家族相似的 DNA 结合表面，但古菌 ParA 超家族通过两个 DNA 结合位点表现出独特的非特异性 DNA 结合。我们通过电子显微镜检测到 HpSpo0J-HpSoj-DNA 复合物，并表明该核基质适应复合物（NAC）是通过 HpSoj 和 HpSpo0J 相互作用和 parS DNA 结合形成的。NAC 的形成通过 HpSoj 的参与和特定 parS DNA 的促进而得到增强。
