The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 10²–10⁴-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.

中文翻译：

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嘧啶特异的核苷水解酶的QM / MM和MM MD模拟：对尿苷酶促水解的全面理解

大肠杆菌的嘧啶特异性核苷水解酶Yeik（CU-NH）用10 ² –10 ⁴裂解尿苷和胞苷的N-糖苷键。速率比嘌呤核苷底物（如肌苷）快两倍。通过使用QM / MM和MM MD模拟研究了尿苷的这种显着的底物特异性和可能的​​水解机理。目前的计算表明，与肌苷相比，尿苷与CU-NH中活性位点残基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-糖苷键裂解方面起着重要作用。 。肌苷水解的估计能量势垒为30 kcal / mol，远远高于尿苷的22 kcal / mol。关于底物向CU-NH活性位点转运的广泛MM MD模拟表明，尿苷结合的放热速率为〜23 kcal / mol，比肌苷（〜12 kcal / mol）更为显着。所有这些都是由底物和CU-NH中的活性位点之间的非共价相互作用引起的，这说明了底物的特异性。与其他核苷水解酶完全不同，此处尿苷的酶促N-糖苷键裂解受质子化的影响较小。