State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 360015, China.
Department of Chemistry, University of California , Davis, California 95616, United States.
J Phys Chem B. 2018 Jan 25;122(3):1121-1131. doi: 10.1021/acs.jpcb.7b10524. Epub 2018 Jan 11.
The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 10-10-fold faster rate than that of purine nucleoside substrates, such as inosine. Such a remarkable substrate specificity and the plausible hydrolytic mechanisms of uridine have been explored by using QM/MM and MM MD simulations. The present calculations show that the relatively stronger hydrogen-bond interactions between uridine and the active-site residues Gln227 and Tyr231 in CU-NH play an important role in enhancing the substrate binding and thus promoting the N-glycosidic bond cleavage, in comparison with inosine. The estimated energy barrier of 30 kcal/mol for the hydrolysis of inosine is much higher than 22 kcal/mol for uridine. Extensive MM MD simulations on the transportation of substrates to the active site of CU-NH indicate that the uridine binding is exothermic by ∼23 kcal/mol, more remarkable than inosine (∼12 kcal/mol). All of these arise from the noncovalent interactions between the substrate and the active site featured in CU-NH, which account for the substrate specificity. Quite differing from other nucleoside hydrolases, here the enzymatic N-glycosidic bond cleavage of uridine is less influenced by its protonation.
大肠杆菌中的嘧啶特异性核苷水解酶 Yeik (CU-NH) 对尿苷和胞苷的 N-糖苷键的切割速度比嘌呤核苷底物（如肌苷）快 10-10 倍。通过使用 QM/MM 和 MM MD 模拟，已经探索了这种显著的底物特异性和尿苷的合理水解机制。本计算表明，与肌苷相比，尿苷与 CU-NH 活性位点残基 Gln227 和 Tyr231 之间相对较强的氢键相互作用在增强底物结合从而促进 N-糖苷键断裂方面起着重要作用。肌苷水解的估计能垒为 30 kcal/mol，远高于尿苷的 22 kcal/mol。对 CU-NH 活性位点底物运输的广泛 MM MD 模拟表明，尿苷的结合是放热的，约为 23 kcal/mol，比肌苷更显著（约 12 kcal/mol）。所有这些都源于 CU-NH 中底物与活性位点之间的非共价相互作用，这解释了底物特异性。与其他核苷水解酶不同，这里尿苷的酶促 N-糖苷键断裂受其质子化的影响较小。
