Márquez-Moñino María Ángeles, Ortega-García Raquel, Shipton Megan L, Franco-Echevarría Elsa, Riley Andrew M, Sanz-Aparicio Julia, Potter Barry V L, González Beatriz
Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.
Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford Mansfield Road, Oxford OX1 3QT, UK.
Sci Adv. 2021 Apr 23;7(17). doi: 10.1126/sciadv.abf6744. Print 2021 Apr.
The yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase DDP1 is a Nudix enzyme with pyrophosphatase activity on diphosphoinositides, dinucleotides, and polyphosphates. These substrates bind to diverse protein targets and participate in signaling and metabolism, being essential for energy and phosphate homeostasis, ATPase pump regulation, or protein phosphorylation. An exhaustive structural study of DDP1 in complex with multiple ligands related to its three diverse substrate classes is reported. This allowed full characterization of the DDP1 active site depicting the molecular basis for endowing multisubstrate abilities to a Nudix enzyme, driven by phosphate anchoring following a defined path. This study, combined with multiple enzyme variants, reveals the different substrate binding modes, preferences, and selection. Our findings expand current knowledge on this important structural superfamily with implications extending beyond inositide research. This work represents a valuable tool for inhibitor/substrate design for DDP1 and orthologs as potential targets to address fungal infections and other health concerns.
酵母双腺苷和二磷酸肌醇多磷酸磷酸水解酶DDP1是一种Nudix酶，对二磷酸肌醇、二核苷酸和多磷酸盐具有焦磷酸酶活性。这些底物与多种蛋白质靶点结合并参与信号传导和代谢，对能量和磷酸盐稳态、ATP酶泵调节或蛋白质磷酸化至关重要。本文报道了对DDP1与与其三种不同底物类别相关的多种配体复合物的详尽结构研究。这使得能够全面表征DDP1活性位点，描绘赋予Nudix酶多底物能力的分子基础，该基础由磷酸盐沿着特定路径锚定驱动。这项研究与多种酶变体相结合，揭示了不同的底物结合模式、偏好和选择。我们的发现扩展了关于这一重要结构超家族的现有知识，其影响超出了肌醇磷脂研究范围。这项工作为DDP1及其直系同源物的抑制剂/底物设计提供了有价值的工具，这些靶点有可能用于解决真菌感染和其他健康问题。
