Department of Chemistry, Yale University, New Haven, Connecticut 06520-8321, United States.
Biochemistry. 2012 Jan 10;51(1):425-32. doi: 10.1021/bi2016662. Epub 2011 Dec 27.
The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacterial signaling pathway. The breakdown of c-di-GMP in the cell is accomplished enzymatically and results in the linear dinucleotide pGpG. The c-di-GMP-binding riboswitches must be able to discriminate between their cognate cyclic ligand and linear dinucleotides in order to be selective biological switches. It has been reported that the c-di-GMP-I riboswitch binds c-di-GMP 5 orders of magnitude better than the linear pGpG, but the cause of this large energetic difference in binding is unknown. Here we report binding data and crystal structures of several linear c-di-GMP analogues in complex with the c-di-GMP-I riboswitch. These data reveal the parameters for phosphate recognition and the structural basis of linear dinucleotide binding to the riboswitch. Additionally, the pH dependence of binding shows that exclusion of pGpG is not due to the additional negative charge on the ligand. These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogues with properties desirable for use as chemical tools and potential therapeutics.
环状二核苷酸 c-di-GMP 调控许多细菌的生活方式转变，例如从自由游动状态到生物膜形成群落的转变。结合这种第二信使的核糖开关是细菌信号通路中的重要下游靶标。细胞内 c-di-GMP 的分解是通过酶促作用完成的，导致线性二核苷酸 pGpG 的产生。c-di-GMP 结合的核糖开关必须能够区分它们的同源环状配体和线性二核苷酸，才能成为选择性的生物开关。据报道，c-di-GMP-I 核糖开关结合 c-di-GMP 的亲和力比线性 pGpG 高 5 个数量级，但结合能产生如此大的能量差异的原因尚不清楚。在这里，我们报告了几个线性 c-di-GMP 类似物与 c-di-GMP-I 核糖开关复合物的结合数据和晶体结构。这些数据揭示了磷酸基识别的参数以及线性二核苷酸与核糖开关结合的结构基础。此外，结合的 pH 依赖性表明，pGpG 的排除不是由于配体上额外的负电荷。这些数据揭示了原则，这些原则与已发表的工作一起，将有助于设计具有作为化学工具和潜在治疗剂所需特性的 c-di-GMP 类似物。
