Prediction of the structure of the complex between the 30S ribosomal subunit and colicin E3 via weighted-geometric docking.
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.
Ben-Zeev
Efrat
E
Weizmann Institute of Science, Department of Biological Chemistry, Rehovot, 76100 Israel.
Zarivach
Raz
R
Shoham
Menachem
M
Yonath
Ada
A
Eisenstein
Miriam
M
D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D020134:Catalytic Domain; D003087:Colicins; D003198:Computer Simulation; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D008958:Models, Molecular; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D021122:Protein Subunits; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism*
D001426:Bacterial Proteins; D003087:Colicins; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D021122:Protein Subunits; C488855:ceiC protein, E coli; C007104:colicin immunity proteins