State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing, 100029, China.
Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008.
J Comput Chem. 2016 May 15;37(13):1163-74. doi: 10.1002/jcc.24306. Epub 2016 Jan 26.
Extensive combined quantum mechanical (B3LYP/6-31G*) and molecular mechanical (QM/MM) molecular dynamics simulations have been performed to elucidate the hydrolytic deamination mechanism of cytosine to uracil catalyzed by the yeast cytosine deaminase (yCD). Though cytosine has no direct binding to the zinc center, it reacts with the water molecule coordinated to zinc, and the adjacent conserved Glu64 serves as a general acid/base to shuttle protons from water to cytosine. The overall reaction consists of several proton-transfer processes and nucleophilic attacks. A tetrahedral intermediate adduct of cytosine and water binding to zinc is identified and similar to the crystal structure of yCD with the inhibitor 2-pyrimidinone. The rate-determining step with the barrier of 18.0 kcal/mol in the whole catalytic cycle occurs in the process of uracil departure where the proton transfer from water to Glu64 and nucleophilic attack of the resulting hydroxide anion to C2 of the uracil ring occurs synchronously. © 2016 Wiley Periodicals, Inc.
采用广泛的量子力学（B3LYP/6-31G*）和经典力学（QM/MM）分子动力学模拟，阐明了酵母胞嘧啶脱氨酶（yCD）催化的胞嘧啶水解脱氨反应机制。尽管胞嘧啶没有直接与锌中心结合，但它与配位到锌上的水分子反应，相邻的保守Glu64 作为广义酸碱，将质子从水中转移到胞嘧啶。整个反应由几个质子转移过程和亲核攻击组成。鉴定到结合锌的胞嘧啶和水分子的四面体型中间体加合物，类似于含抑制剂 2-嘧啶酮的 yCD 的晶体结构。在整个催化循环中，速率决定步骤的势垒为 18.0 kcal/mol，发生在尿嘧啶离去过程中，水到 Glu64 的质子转移和生成的氢氧根阴离子对尿嘧啶环 C2 的亲核攻击同时发生。© 2016 Wiley Periodicals, Inc.
