Active sites in Escherichia coli ribosomes

Abstract

In the figure, 30 S ribosomal proteins have been arranged according to their functional role: Protein S1 is required for mRNA binding. Proteins S3, S4, S5, S11 and S12 are involved in cistron and/or codon—anticodon recognition. They must be close to the decoding sites on the 30 S subunit. Furthermore proteins S2, S3, S10, S14, S19 and S21 function in f-Met-tRNA binding. Proteins S1, S2, S3, S10, S14, S19, S20 and S21 are important for the function of both decoding sites, whereas proteins S9, S11 and S18 are only needed for EF—Tu-dependent aminoacyl-tRNA binding. Proteins S2, S5, S9 and S11 would be close to the GTPase center of the 50 S subunit, since they are important for this activity. The present available data concerning the 50 S subunit allow the following picture to be drawn: Protein L16 is involved in binding the 3′-terminus of aminoacyl-tRNA in the A-site. Next to it in the A-site, there is protein L6. The P-site is located adjacent to the A-site of the peptidyltransferase center. Accordingly, protein L2 is near protein L6 and is located in the P-site as well as proteins L27 and L4. Protein L11, which is intimately involved in peptide bond formation, would have to border parts of both A- and P-sites. Proteins L6 and L2 stimulate binding of 5 S RNA—protein complexes to 23 S RNA. The 5 S RNA—protein complex has GTPase and ATPase activities. The proteins in this complex (L5, L18, L20, L25 and L30) seem to be located close to the A-site of the peptidyltransferase center. These proteins together with protein L11 are involved in GDP binding. Proteins L10 and L6 are implicated in reconstitution of protein L7 and L12 mediated EF—G-dependent ribosomal GTP hydrolysis. This observation is supported by the fact that the aminoacyl-tRNA binding site, e.g. proteins L16 and L6, is connected with EF—G and EF—Tu binding site, e.g. proteins L7 and L12, as well as the GTPase center. Furthermore, if one of the functional roles of 5 S RNA is to bind aminoacyl-tRNA via T—Ψ—C, then those ribosomal proteins which bind to 5 S RNA (or are close to it) would be located near or at the A-site. The model of active sites in E. coli ribosome illustrated in the figure is based on the presently available experimental results. It is far from being complete and should not be overinterpreted as an accurate topographical model. More data on the functional role of ribosomal components and on the topography of the subunits can be expected in the near future and will add to the knowledge on the active sites in ribosomes.