Structural Basis of the Ribosomal Machinery for Peptide Bond Formation, Translocation, and Nascent Chain Progression

Abstract

Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3' end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism.

Functional aspects of ribosomal architecture: symmetry, chirality and regulation

“…These are the multi-task inter-subunit bridge B2a [Plate 1(f)] that is likely to assist the A-to P-site tRNA acceptor-stem shift, 11,21 and the PTC nucleotide A2602 (Escherichia coli nomenclature is being used throughout) that seems to be involved in A-to P-translocation within the PTC. 8,9,11 The PTC itself possesses the dynamic properties required for facilitating the correctly bound A-site tRNA to the P-site and for assisting rearrangements of less well aligned substrates. 8,9,11,21 It is located close to the subunit interface, at the bottom of a cavity in the large ribosomal subunit.…”

“…8,9,11 The PTC itself possesses the dynamic properties required for facilitating the correctly bound A-site tRNA to the P-site and for assisting rearrangements of less well aligned substrates. 8,9,11,21 It is located close to the subunit interface, at the bottom of a cavity in the large ribosomal subunit. The peripheral upper rim of this cavity includes a ribosomal protein, L16, but the PTC itself is formed exclusively by ribosomal RNA [Plate (1b-d)].…”

“…Crystallography of ribosomes, initiated over two decades ago 1 recently yielded several three-dimensional structures of free and complexes ribosomal particles [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] and enabled the assignments of the three tRNA binding sites on each of the ribosomal subunits to be made [plate 1(a) and (b)]. They also confirmed the notion that the main parts of the A-and P-site tRNA molecules are roughly parallel to each other, whereas the E-site tRNA has to rotate while exiting the ribosome.…”

“…[12][13][14][15][16] The findings presented in this review are based mainly on the high-resolution structures of the small ribosomal subunit from Thermus thermophilus T30S 4 [Plate 1(a)] and the large ribosomal subunit from D. radiodurans, D50S, in its free form 7 [Plate 1(b)] as well as in complexes with various mimics of aminoacylated tRNA molecules. 8 Here, we discuss some of the latest advances in the understanding of the molecular basis of the catalytic mechanism of peptide bond formation, and of the ribosomal action as an amino acid polymerase. We also analyze the ribosomal architecture and highlight selected ribosomal regulatory tasks.…”

The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli

“…This region has been shown to be part of the peptidyltransferase center (PTC). Based on the crystal structures of Thermus thermophilus 70S ribosomes (Yusupov et al 2001) and Deinococcus radiodurans 50S rRNA (Bashan et al 2003;Yonath and Bashan 2004) and cryo-electron microscopy mapping of E. coli 70S ribosomes (Agrawal et al 2004) complexed with various substrates, domain IV and helix 69 (including C1915; Agrawal et al 2004) are known to interact with mRNA, tRNAs, 16S rRNA, and Ribosomal Release Factor, and may be involved in proper tRNA positioning, in translocation, and in release of mRNA from the posttermination complex. Taken together, these findings suggest that helix 69 and the modified residues of 23S rRNA are important for efficient protein biosynthesis by the ribosome.…”