The Structural Basis of Ribosome Activity in Peptide Bond Synthesis

Abstract

Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K(a) is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.

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“…Thus, the Tim23 channel is not simply a cylindrical pore; rather, its internal and external diameters differ considerably. At its narrowest point, the Tim23 channel is smaller than both the Tom40 channel 5,6,26 and the functional translocon of the endoplasmic reticulum (∼20-50 Å) [30][31][32] but is similar to the average diameter of the polypeptide exit channel of the ribosome large subunit (15 Å) 33 . The restriction zone diameter of the Tim23 channel is just large enough to accommodate one polypeptide chain in an α-helical conformation but not large enough to contain two α-helices at the same time.…”

Representation, searching and discovery of patterns of bases in complex RNA structures

“…A GG platform is found in the structure of domain V of H.marismortui large ribosomal subunit RNA (G2616.G2617) and both guanines are highly conserved in archaea. This is at a key position in the peptidyl transferase centre, base numbers 2618 to 2620 are all implicated in substrate binding as they have been shown to interact with substrate analogues incorporating the CCA portion of A site tRNA [49]. The structural role of the platform may be that it creates a space within the cavity for the subsequent bases to interact with the substrate.…”

Teaching argumentation and scientific discourse using the ribosomal peptidyl transferase reaction

“…1A) [1]. Francis Crick had hypothesized in 1968 that the ribosome was actually a ribozyme, but until 2000, only limited evidence supported this theory [2].…”

“…The structure of the ribosome solidified the assertion that the ribosome was a ribozyme, as no amino acid lay closer than 17 Å to the site of peptidyl transfer (Figs. 1C and 1D) [1,3]. The question then became how RNA could accomplish peptide bond synthesis, and the structure of the large ribosomal subunit bound to a transition state mimic ignited a flurry of activity to provide a detailed molecular explanation of the peptidyl transferase reaction (Fig.…”