8EIU

E. coli 70S ribosome with A-loop mutations U2554C and U2555C

This is a non-PDB format compatible entry.

Summary for 8EIU

• Entry DOI: 10.2210/pdb8eiu/pdb
• EMDB information: 28165 28218 28229 28230
• Descriptor: 50S ribosomal protein L33, 30S ribosomal protein S5, 30S ribosomal protein S6, ... (62 entities in total)
• Functional Keywords: rna, thermophile, a loop, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 55
• Total formula weight: 2208400.96

Authors

Nissley, A.J.,Penev, P.I.,Watson, Z.L.,Banfield, J.F.,Cate, J.H.D. (deposition date: 2022-09-15, release date: 2023-02-01, Last modification date: 2023-11-15)

Primary citation

Nissley, A.J.,Penev, P.I.,Watson, Z.L.,Banfield, J.F.,Cate, J.H.D.
Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome.
Nucleic Acids Res., 51:1880-1894, 2023

PubMed Abstract: The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.

PubMed: 36660825
DOI: 10.1093/nar/gkac1273

Experimental method

ELECTRON MICROSCOPY (2.24 Å)