Atypical Response Regulator ChxR from Chlamydia trachomatis Is Structurally Poised for DNA Binding

ChxR is an atypical two-component signal transduction response regulator (RR) of the OmpR/PhoB subfamily encoded by the obligate intracellular bacterial pathogen Chlamydia trachomatis. Despite structural homology within both receiver and effector domains to prototypical subfamily members, ChxR does not require phosphorylation for dimer formation, DNA binding or transcriptional activation. Thus, we hypothesized that ChxR is in a conformation optimal for DNA binding with limited interdomain interactions. To address this hypothesis, the NMR solution structure of the ChxR effector domain was determined and used in combination with the previously reported ChxR receiver domain structure to generate a full-length dimer model based upon SAXS analysis. Small-angle scattering of ChxR supported a dimer with minimal interdomain interactions and effector domains in a conformation that appears to require only subtle reorientation for optimal major/minor groove DNA interactions. SAXS modeling also supported that the effector domains were in a head-to-tail conformation, consistent with ChxR recognizing tandem DNA repeats. The effector domain structure was leveraged to identify key residues that were critical for maintaining protein - nucleic acid interactions. In combination with prior analysis of the essential location of specific nucleotides for ChxR recognition of DNA, a model of the full-length ChxR dimer bound to its cognate cis-acting element was generated.

ChxR是专性胞内病原菌沙眼衣原体（Chlamydia trachomatis）编码的OmpR/PhoB亚家族非典型双组分信号转导应答调控蛋白（response regulator, RR）。尽管其接收域与效应域在结构上与该亚家族的典型成员具有同源性，但ChxR无需磷酸化即可完成二聚化、DNA结合及转录激活。据此我们提出假说：ChxR处于一种域间相互作用有限的DNA结合最优构象。为验证这一假说，我们解析了ChxR效应域的核磁共振（NMR）溶液结构，并结合此前已报道的ChxR接收域结构，基于小角X射线散射（SAXS）分析构建了全长二聚体模型。小角散射实验结果证实，ChxR以域间相互作用极小的二聚体形式存在，其效应域构象仅需轻微重定向，即可实现与DNA大沟/小沟的最优相互作用。SAXS建模结果还显示，效应域呈头对尾构象，这与ChxR识别串联DNA重复序列的特性相符。我们依托该效应域结构，鉴定出了维持蛋白质-核酸相互作用的关键残基。结合此前关于ChxR识别DNA所需特定核苷酸必需位点的研究，我们构建了结合其同源顺式作用元件的全长ChxR二聚体模型。