Functional aspects of ribosomal architecture: symmetry, chirality and regulation

Abstract

Abstract High‐resolution structures of both ribosomal subunits revealed that most stages of protein biosynthesis, including decoding of genetic information, are navigated and controlled by the elaborate ribosomal architectural‐design. Remote interactions govern accurate substrate alignment within a flexible active‐site pocket [peptidyl transferase center (PTC)], and spatial considerations, due mainly to a universal mobile nucleotide, U2585, ensure proper chirality by interfering with D ‐amino‐acids incorporation. tRNA translocation involves two correlated motions: overall mRNA/tRNA (messenger and transfer RNA) shift, and a rotation of the tRNA single‐stranded aminoacylated‐3′ end around the bond connecting it with the tRNA helical‐regions. This bond coincides with an axis passing through a sizable symmetry‐related region, identified around the PTC in all large‐subunit crystal structures. Propelled by a bulged universal nucleotide, A2602, positioned at the two‐fold symmetry axis, and guided by a ribosomal‐RNA scaffold along an exact pattern, the rotatory motion results in stereochemistry optimal for peptide‐bond formation and in geometry ensuring nascent proteins entrance into their exit tunnel. Hence, confirming that ribosomes contribute positional rather than chemical catalysis, and that peptide bond formation is concurrent with A‐ to P‐site tRNA passage. Connecting between the PTC, the decoding center, the tRNA entrance and exit points, the symmetry‐related region can transfer intra‐ribosomal signals between remote functional locations, guaranteeing smooth processivity of amino acids polymerization. Ribosomal proteins are involved in accurate substrate placement (L16), discrimination and signal transmission (L22) and protein biosynthesis regulation (CTC). Residing on the exit tunnel walls near its entrance, and stretching to its opening, protein‐L22 can mediate ribosome response to cellular regulatory signals, since it can swing across the tunnel, causing gating and elongation arrest. Each of the protein CTC domains has a defined task. The N ‐terminal domain stabilizes the intersubunit‐bridge confining the A‐site‐tRNA entrance. The middle domain protects the bridge conformation at elevated temperatures. The C ‐terminal domain can undergo substantial conformational rearrangements upon substrate binding, indicating CTC participation in biosynthesis‐control under stressful conditions. Copyright © 2004 John Wiley & Sons, Ltd.