m l27 l2


sites for these tRNAs, shows that the PTC region of 23 S rRNA as a whole is compactly folded. For example, the A-site-bound tRNA protects from chemical modification residues A2451 and U2609 that are quite distant in the rRNA primary (and secondary) structure. Other tRNA protection sites are scattered around the PTC ring. Also, the P-site-bound tRNA cross-links to U2584/U2585 and to A2451 located on the "opposite" sides of the ring. Moreover, the P-site-bound tRNA strongly protects the highly conserved residues G2252 and G2253 outside the PTC ring, in the end loop of the short hairpin 2246-2258 of donain V (see Fig. 6.5). The latter protection is dependent on the presence of the universal 3'-terminal sequence of tRNA. There is experimental evidence that G2252 participates in fixation of the 3'-end sequence CCA of the P-site-bound tRNA in PTC due to Watson-Crick base-pairing with C74 of the tRNA (Samaha et al., 1995).

The formation of a special compact tertiary structure expected in the PTC region seems to be critical for the activity. It is likely that PTC is organized mainly by self-folding of domain V of the 23S RNA. At the same time, the relevant ribosomal proteins may contribute to stabilization of the proper structure of the peptidyl transferase region and the entire domain V. In any case, up to now nobody was able to prove unequivocally that protein-free 23S rRNA can catalyze peptide bond formation.

Localization of PTC on the morphologically visible surfaces of the 50S subunit can be done from knowing the proteins which are complexed with the sequence 2450-2600 of the 23S RNA domain V, and from immuno-electron microscopic detection of specific substrates or inhibitors of the peptidyl transferase center (see Stoeffler & Stoeffler-Meilicke, 1984). The protein L27 has been found to form multiple crosslinks with this sequence, and at the same time it has been detected by immuno-electron microscopy under the central protuberance, in the region of the groove ("neck") between it and the rest of the 50S subunit body. Puromycin derivatives as substrates of the peptidyl transferase are also detected under the central protuberance, but more at the side of the L1 ridge. The same place has been indicated by detection of bound inhibitors, such as chloramphenicol and lincomycin.

On the whole, it can be stated that PTC is located at the 50S subunit, on its interface (concave) side, under the head (central protuberance), and more exactly in the region of the groove separating the head from the rest of the body. The likely position of PTC on the 50S ribosomal subunit is shown schematically in Fig. 9.8.

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