|Pseudoknot of the domain G(G12) of 23S ribosomal RNA|
|RNA type||Gene; rRNA|
The 23S rRNA is a 2904 nt long (in E. coli) component of the large subunit (50S) of the bacterial/archean ribosome. The ribosomal peptidyl transferase activity resides in domain V of this rRNA, and this domain is the most common binding site for antibiotics that inhibit translation. A well-known member of this antibiotic class, chloramphenicol, acts by inhibiting peptide bond formation, with recent 3D-structural studies showing two different binding sites depending on the species of ribosome. Linezolid and quinupristin-dalfopristin also bind to the 23S rRNA, and cross-resistance has been demonstrated between these antibiotics. Compared to 16S rRNA genes, 23S rRNA genes typically have higher sequence variations including insertions and/or deletions.
In general, rRNA has an essential function of peptidyl transferase, the stimulating core of the ribosome plays role in the peptide bond configuration. Both peptidyl-tRNA and aminoacyl-tRNA are important for synthesizing protein and transpeptidation response. However, 23S rRNA positions which are G2252, A2451, U2506, and U2585 have a significant function for tRNA binding in P site of the large ribosomal subunit. These modification nucleotides in site P can inhibit peptidyl-tRNA from binding and also remains U2555 modification intervene with transferring peptidyl-tRNA to puromycin. Furthermore, the chemical modification of half of these positions G2251, G2253, A2439, and U2584 can not prevent the tRNA binding. Peptidyl-tRNA of 50s subunits which binds to the P site preserve eight positions of 23S rRNA from chemical modification. On the other hand, 23S rRNA impacts on mutation for cell growth. Mutations A1912G, A1919G and Ψ1917C have a powerful growth phenotypes and they prevent translation while mutation A1916G has a simple growth phenotype and it leads to defect in the 50S subunits.
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