Xiao Jing-fa, Li Ze-sheng, Sun Chia-chung
Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, PR China.
Bioorg Med Chem. 2004 May 1;12(9):2035-41. doi: 10.1016/j.bmc.2004.02.038.
The novel C3-like ADP-ribosyltransferase is produced by a Staphylococcus aureus strain that especially ADP-ribosylates RhoE/Rnd3 subtype proteins, and its three-dimensional (3D) structure has not known. In order to understand the catalytic mechanism, the 3D structure of the protein is built by using homology modeling based on the known crystal structure of exoenzyme C3 from Clostridium botulinum (1G24). Then the model structure is further refined by energy minimization and molecular dynamics methods. The putative nicotinamide adenine dinucleotide (NAD(+))-binding pocket of exoenzyme C3(Stau) is determined by Binding-Site Search module. The NAD(+)-enzyme complex is developed by molecular dynamics simulation and the key residues involved in the combination of enzyme binding to the ligand-NAD(+) are determined, which is helpful to guide the experimental realization and the new mutant designs as well. Our results indicated that the key binding-site residues of Arg48, Glu180, Ser138, Asn134, Arg85, and Gln179 play an important role in the catalysis of exoenzyme C3(Stau), which is in consistent with experimental observation.
这种新型的C3样ADP核糖基转移酶由一株金黄色葡萄球菌产生，该菌株特别能使RhoE/Rnd3亚型蛋白发生ADP核糖基化，其三维（3D）结构尚不清楚。为了了解其催化机制，基于肉毒梭菌外切酶C3的已知晶体结构（1G24），通过同源建模构建了该蛋白的3D结构。然后通过能量最小化和分子动力学方法对模型结构进行进一步优化。利用结合位点搜索模块确定了外切酶C3（Stau）假定的烟酰胺腺嘌呤二核苷酸（NAD(+)）结合口袋。通过分子动力学模拟构建了NAD(+) - 酶复合物，并确定了酶与配体NAD(+)结合过程中涉及的关键残基，这也有助于指导实验实现和新的突变体设计。我们的结果表明，Arg48、Glu180、Ser138、Asn134、Arg85和Gln179等关键结合位点残基在外切酶C3（Stau）的催化中起重要作用，这与实验观察结果一致。
