Wu Xian-Hui, Quan Jun-Min, Wu Yun-Dong
Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China.
J Phys Chem B. 2007 Jun 7;111(22):6236-44. doi: 10.1021/jp068611m. Epub 2007 May 11.
The reaction pathway of deformylation catalyzed by E. coli peptide deformylase (PDF) has been investigated by the density functional theory method of PBE1PBE on a small model and by a two-layer ONIOM method on a realistic protein model. The deformylation proceeds in sequential steps involving nucleophilic addition of metal-coordinated water/hydroxide to the carbonyl carbon of the formyl group, proton transfer, and cleavage of the C-N bond. The first step is rate-determining for the deformylation, which occurs through a pentacoordinated metal center. The estimated activation energies with the ONIOM method are about 23.0, 15.0, and 14.9 kcal/mol for Zn-, Ni-, and Fe-PDFs, respectively. These calculated barriers are in close agreement with experimental observations. Our results demonstrate that the preference for metal coordination geometry exerts a significant influence on the catalytic activity of PDFs by affecting the activation of the carbonyl group of the substrate, the deprotonation of the metal-coordinated water, and the stabilization of the transition state. This preference for coordination geometry is mainly determined by the ligand environment and the intrinsic electronic structures of the metal center in the active site of the PDFs.
通过在小模型上采用PBE1PBE的密度泛函理论方法以及在实际蛋白质模型上采用双层ONIOM方法，研究了大肠杆菌肽脱甲酰基酶（PDF）催化的脱甲酰基反应途径。脱甲酰基反应按顺序进行，包括金属配位的水/氢氧根对甲酰基羰基碳的亲核加成、质子转移以及C-N键的断裂。第一步是脱甲酰基反应的速率决定步骤，它通过五配位金属中心发生。采用ONIOM方法估计的Zn-PDF、Ni-PDF和Fe-PDF的活化能分别约为23.0、15.0和14.9 kcal/mol。这些计算出的能垒与实验观察结果密切相符。我们的结果表明，对金属配位几何结构的偏好通过影响底物羰基的活化、金属配位水的去质子化以及过渡态的稳定性，对PDF的催化活性产生显著影响。这种对配位几何结构的偏好主要由PDF活性位点中金属中心的配体环境和固有电子结构决定。
