(p)ppGpp is a nucleotide messenger universally produced in bacteria following nutrient starvation. In E. coli, ppGpp inhibits purine nucleotide synthesis by targeting several different enzymes, but the physiological significance of their inhibition is unknown. Here, we report the structural basis of inhibition for one target, Gsk, the inosine-guanosine kinase. Gsk creates an unprecedented, allosteric binding pocket for ppGpp by restructuring terminal sequences, which restrains conformational dynamics necessary for catalysis. Guided by this structure, we generated a chromosomal mutation that abolishes Gsk regulation by ppGpp. This mutant strain accumulates abnormally high levels of purine nucleotides following amino-acid starvation, compromising cellular fitness. We demonstrate that this unrestricted increase in purine nucleotides is detrimental because it severely depletes pRpp and essential, pRpp-derived metabolites, including UTP, histidine, and tryptophan. Thus, our results reveal the significance of ppGpp’s regulation of purine nucleotide synthesis and a critical mechanism by which E. coli coordinates biosynthetic processes during starvation.

(p)ppGpp 是一种核苷酸信使，通常在营养饥饿后在细菌中产生。在大肠杆菌中, ppGpp 通过靶向几种不同的酶来抑制嘌呤核苷酸的合成，但其抑制的生理意义尚不清楚。在这里，我们报告了一个目标，Gsk，肌苷-鸟苷激酶抑制的结构基础。Gsk 通过重组末端序列为 ppGpp 创建了一个前所未有的变构结合口袋，这限制了催化所需的构象动力学。在这种结构的指导下，我们产生了一个染色体突变，该突变消除了 ppGpp 对 Gsk 的调控。这种突变菌株在氨基酸饥饿后会积累异常高水平的嘌呤核苷酸，从而损害细胞健康。我们证明嘌呤核苷酸的这种不受限制的增加是有害的，因为它严重消耗了 pRpp 和必需的 pRpp 衍生代谢物，包括 UTP、组氨酸、和色氨酸。因此，我们的结果揭示了 ppGpp 调控嘌呤核苷酸合成的重要性以及一个关键机制大肠杆菌在饥饿期间协调生物合成过程。