Prediction of the Structure of the Complex Between the 30S Ribosomal Subunit and Colicin E3 via Weighted-Geometric Docking |
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Authors: | Efrat Ben-Zeev Raz Zarivach Menachem Shoham Ada Yonath Miriam Eisenstein |
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Institution: | 1. Weizmann Institute of Science, Department of Biological Chemistry , Rehovot , 76100 , Israel;2. Weizmann Institute of Science, Department of Structural Biology , Rehovot , 76100 , Israel;3. Case Western Reserve University School of Medicine, Department of Biochemistry , Cleveland , OH , 44106-4935 , USA;4. Weizmann Institute of Science, Department of Structural Biology , Rehovot , 76100 , Israel;5. Max-Planck-Research Unit for Ribosomal Structure , Notkestrasse 85, 22603 , Hamburg , Germany;6. Weizmann Institute of Science, Department of Chemical Services , Rehovot , 76100 , Israel |
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Abstract: | Abstract 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. |
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