Polypeptide exit tunnel, ribosome

According to Nissen et al. [27], proteins L4, L22, and L39e (the letter e represents a protein in a bacterial SOS ribosomal subunit, a protein that belongs to one of the homologs in eukaryotic 60S ribosomal subunit) have been shown to be present in the polypeptide exit tunnel [average diameter, about IS A length of the tunnel, 100 A (Fig. 3B)] present in the SOS ribosomal subunit from H. maris-mortui. Six other proteins (L19, L22, L23, L24, L29, and L31e) are known to be located in the exit area of the polypeptide tunnel [26, 27]. If these proteins are involved in the inhibitory actions of macrolide antibiotics, mutant bacteria resistant to macrolides will develop in the future. 

The macrolides inhibit bacteria by interfering with programmed ribosomal protein biosynthesis by binding to the 23S rRNA in the polypeptide exit tunnel adjacent to the peptidyl transferase center in the SOS subparticle (Fig. 38.24). Binding appears to occur at two specific regions within the rRNA, which are referred to as domain V at adenine 2058 and 2059 and domain II... 

The peptidyl transferase centre of the ribosome is located in the 50S subunit, in a protein-free environment (there is no protein within 15 A of the active site), supporting biochemical evidence that the ribosomal RNA, rather than the ribosomal proteins, plays a key role in the catalysis of peptide bond formation. This confirms that the ribosome is the largest known RNA catalyst (ribozyme) and, to date, the only one with synthetic activity. Adjacent to the peptidyl transferase centre is the entrance to the protein exit tunnel, through which the growing polypeptide chain moves out of the ribosome. 

A major feature observed on the 508 subunit stmc-ture is an apparent tunnel through the center of the subunit, through which the newly synthesized polypeptide is proposed to exit the ribosome. The tunnel seems to be wide enough to accommodate the polypeptide, and extends from the peptidyl transferase center to A-site on the back (solvent side) of the 508 subunit. 

The proteins in a ribosome may help to hold the RNA into conformations that are correct for its functions. They may also catalyze conformational alterations during the various steps of the translation process. In addition, the proteins may help provide binding sites for substrate molecules and participate in regulatory activities. Both the tRNA exit (E) site and the tunnel through which the polypeptide chain leaves the ribosome are composed, in part, of ribo-somal proteins. 

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