4V97

Crystal structure of the bacterial ribosome ram mutation G299A.

This is a non-PDB format compatible entry.

Summary for 4V97

• Entry DOI: 10.2210/pdb4v97/pdb
• Descriptor: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (59 entities in total)
• Functional Keywords: protein biosynthesis, ribosomes, rna, trna, transfer, ribosomal ambiguity mutation, ram, 30s, 70s, 16s, ribosomal subunit, ribosome
• Biological source: Thermus thermophilus; More
• Total number of polymer chains: 114
• Total formula weight: 4576932.51

Authors

Fagan, C.E.,Dunkle, J.A.,Maehigashi, T.,Dunham, C.M. (deposition date: 2012-04-06, release date: 2014-07-09, Last modification date: 2023-09-20)

Primary citation

Fagan, C.E.,Dunkle, J.A.,Maehigashi, T.,Dang, M.N.,Devaraj, A.,Miles, S.J.,Qin, D.,Fredrick, K.,Dunham, C.M.
Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.
Proc.Natl.Acad.Sci.USA, 110:9716-9721, 2013

PubMed Abstract: After four decades of research aimed at understanding tRNA selection on the ribosome, the mechanism by which ribosomal ambiguity (ram) mutations promote miscoding remains unclear. Here, we present two X-ray crystal structures of the Thermus thermophilus 70S ribosome containing 16S rRNA ram mutations, G347U and G299A. Each of these mutations causes miscoding in vivo and stimulates elongation factor thermo unstable (EF-Tu)-dependent GTP hydrolysis in vitro. Mutation G299A is located near the interface of ribosomal proteins S4 and S5 on the solvent side of the subunit, whereas G347U is located 77 Å distant, at intersubunit bridge B8, close to where EF-Tu engages the ribosome. Despite these disparate locations, both mutations induce almost identical structural rearrangements that disrupt the B8 bridge--namely, the interaction of h8/h14 with L14 and L19. This conformation most closely resembles that seen upon EF-Tu-GTP-aminoacyl-tRNA binding to the 70S ribosome. These data provide evidence that disruption and/or distortion of B8 is an important aspect of GTPase activation. We propose that, by destabilizing B8, G299A and G347U reduce the energetic cost of attaining the GTPase-activated state and thereby decrease the stringency of decoding. This previously unappreciated role for B8 in controlling the decoding process may hold relevance for many other ribosomal mutations known to influence translational fidelity.

PubMed: 23630274
DOI: 10.1073/pnas.1301585110

Experimental method

X-RAY DIFFRACTION (3.516 Å)