Ribosomal crystallography: a flexible nucleotide anchoring tRNA translocation, facilitates peptide‐bond formation, chirality discrimination and antibiotics synergism

Abstract

The linkage between internal ribosomal symmetry and transfer RNA (tRNA) positioning confirmed positional catalysis of amino-acid polymerization. Peptide bonds are formed concurrently with tRNA-3 0 end rotatory motion, in conjunction with the overall messenger RNA (mRNA)/tRNA translocation. Accurate substrate alignment, mandatory for the processivity of protein biosynthesis, is governed by remote interactions. Inherent flexibility of a conserved nucleotide, anchoring the rotatory motion, facilitates chirality discrimination and antibiotics synergism. Potential tRNA interactions explain the universality of the tRNA CCA-end and P-site preference of initial tRNA. The interactions of protein L2 tail with the symmetry-related region periphery explain its conservation and its contributions to nascent chain elongation.

Ribosome crystallography: catalysis and evolution of peptide-bond formation, nascent chain elongation and its co-translational folding

“…Unlike enzymes catalysing a single chemical reaction, such as proteases, and similar to other polymerases, the ribosome provides the means for substrate motions required for the processivity of peptide-bond formation, namely for amino acid polymerization [20,21]. In the present study, we show that the ribosomal architectural in blue and the P-site in green.…”

“…In addition, for initiating the rotatory motion, the initial P-site tRNA should acquire its functional orientation. Having two guanines at the P-site, compared with one at the A-site, seem to fulfil this requirement [21,22]. It appears therefore that the ribosomal architectural-frame governs the catalytic positional requirements and provides the means for the chemical catalysis.…”

Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions

“…Supporting evidence is provided by DMS-protection experiments, indicating that helices H42–H44 in complex C achieve a tighter structure upon ABA-spermine photo-incorporation. Another observation that can explain the effect of polyamines on tRNA translocation is related with the labeling of A2602 and U2584 residues in the central loop of domain V. Next to U2584 is U2585, which along with A2602 bulge into the PTase center, close to the symmetry axis of the catalytic cavity (3,6,53). Both U2585 and A2602 have been envisaged to play a dynamic role in the passage of the tRNA-3′ end from the A- to the P-site; A2602 has been proposed to propel, in concert with the tip of helix H69, the rotatory motion of the tRNA-3′ end, while U2585 has been suggested to anchor the rotatory motion by direct interaction with the tRNA-bound amino acid and assure the proper positioning of P-site substrates (53).…”

“…Another observation that can explain the effect of polyamines on tRNA translocation is related with the labeling of A2602 and U2584 residues in the central loop of domain V. Next to U2584 is U2585, which along with A2602 bulge into the PTase center, close to the symmetry axis of the catalytic cavity (3,6,53). Both U2585 and A2602 have been envisaged to play a dynamic role in the passage of the tRNA-3′ end from the A- to the P-site; A2602 has been proposed to propel, in concert with the tip of helix H69, the rotatory motion of the tRNA-3′ end, while U2585 has been suggested to anchor the rotatory motion by direct interaction with the tRNA-bound amino acid and assure the proper positioning of P-site substrates (53). Also, strong cross-linking of ABA-spermine occurs into the tip and the internal loop of H89, a helix previously detected to interact with EFG (52), the L7/L12 stalk (54) and 5S rRNA (55).…”

Modulation of Catalytic RNA Biological Activity by Small Molecule Effectors

“…Dalfopristin binds directly within the peptidyl transferase center affecting both A-and P-site occupation by the tRNA molecules. The streptogramin complex with the Deinococcus 50S subunit reveals a localized conformational change of the peptidyl transferase center in the orientation of residue U2585, which has been hypothesized as a source of the bactericidal activity and the postantibiotic effect of the Synecrid ® combination [51,52].…”