Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan.
RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
Acta Crystallogr F Struct Biol Commun. 2024 Oct 1;80(Pt 10):278-285. doi: 10.1107/S2053230X2400877X. Epub 2024 Sep 18.
Guanosine 5'-monophosphate (GMP) synthetase (GuaA) catalyzes the last step of GMP synthesis in the purine nucleotide biosynthetic pathway. This enzyme catalyzes a reaction in which xanthine 5'-monophosphate (XMP) is converted to GMP in the presence of Gln and ATP through an adenyl-XMP intermediate. A structure of an XMP-bound form of GuaA from the domain Bacteria has not yet been determined. In this study, the crystal structure of an XMP-bound form of GuaA from the thermophilic bacterium Thermus thermophilus HB8 (TtGuaA) was determined at a resolution of 2.20 Å and that of an apo form of TtGuaA was determined at 2.10 Å resolution. TtGuaA forms a homodimer, and the monomer is composed of three domains, which is a typical structure for GuaA. Disordered regions in the crystal structure were obtained from the AlphaFold2-predicted model structure, and a model with substrates (Gln, XMP and ATP) was constructed for molecular-dynamics (MD) simulations. The structural fluctuations of the TtGuaA dimer as well as the interactions between the active-site residues were analyzed by MD simulations.
鸟苷 5'-单磷酸（GMP）合成酶（GuaA）催化嘌呤核苷酸生物合成途径中 GMP 合成的最后一步。该酶催化在 Gln 和 ATP 的存在下，通过腺嘌呤核苷酸-XMP 中间体，将黄嘌呤 5'-单磷酸（XMP）转化为 GMP 的反应。尚未确定来自域细菌的 XMP 结合形式的 GuaA 的结构。在这项研究中，测定了嗜热细菌 Thermus thermophilus HB8（TtGuaA）的 XMP 结合形式的 GuaA 的晶体结构，分辨率为 2.20 Å，以及 TtGuaA 的 apo 形式的晶体结构，分辨率为 2.10 Å。TtGuaA 形成同源二聚体，单体由三个结构域组成，这是 GuaA 的典型结构。晶体结构中的无规卷曲区域是从 AlphaFold2 预测的模型结构中获得的，并构建了带有底物（Gln、XMP 和 ATP）的模型，用于分子动力学（MD）模拟。通过 MD 模拟分析了 TtGuaA 二聚体的结构波动以及活性位点残基之间的相互作用。
