Ben-Zeev Efrat, Zarivach Raz, Shoham Menachem, Yonath Ada, Eisenstein Miriam
Weizmann Institute of Science, Department of Biological Chemistry, Rehovot, 76100 Israel.
J Biomol Struct Dyn. 2003 Apr;20(5):669-76. doi: 10.1080/07391102.2003.10506883.
Colicin E3 kills Escherichia coli cells by ribonucleolytic cleavage in the 16S rRNA. The cleavage occurs at the ribosomal decoding A-site between nucleotides A1493 and G1494. The breaking of this single phosphodiester bond results in a complete termination of protein biosynthesis leading to cell death. A model structure of the complex of the ribosomal subunit 30S and colicin E3 was constructed by means of a new weighted-geometric docking algorithm, in which interactions involving specified parts of the molecular surface can be up-weighted, allowing incorporation of experimental data in the docking search. Our model, together with available experimental data, predicts the role of the catalytic residues of colicin E3. In addition, it suggests that bound acidic immunity protein inhibits the enzymatic activity of colicin E3 by electrostatic repulsion of the negatively charged substrate.
大肠杆菌素E3通过对16S rRNA进行核糖核酸酶切割来杀死大肠杆菌细胞。切割发生在核糖体解码A位点的核苷酸A1493和G1494之间。这个单一磷酸二酯键的断裂导致蛋白质生物合成完全终止，从而导致细胞死亡。利用一种新的加权几何对接算法构建了核糖体亚基30S与大肠杆菌素E3复合物的模型结构，在该算法中，涉及分子表面特定部分的相互作用可以被加权，从而在对接搜索中纳入实验数据。我们的模型与现有实验数据一起预测了大肠杆菌素E3催化残基的作用。此外，它表明结合的酸性免疫蛋白通过对带负电荷底物的静电排斥来抑制大肠杆菌素E3的酶活性。
