5DFE

70S termination complex containing E. coli RF2

This is a non-PDB format compatible entry.

Summary for 5DFE

• Entry DOI: 10.2210/pdb5dfe/pdb
• Related: 5CZP
• Descriptor: P-site tRNA fMet, 50S ribosomal protein L6, 50S ribosomal protein L9, ... (58 entities in total)
• Functional Keywords: protein biosynthesis, ribosomes, rna, trna, transfer rna, 30s, 50s, 70s, 16s, 23s, ribosomal subunit, rf2, release factor 2, peptide chain termination, release factor, bacterial proteins, codon, molecular peptide chain termination, translational, ribosome
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 110
• Total formula weight: 4552148.28

Authors

Hoffer, E.D.,Dunham, C.M. (deposition date: 2015-08-26, release date: 2016-10-12, Last modification date: 2023-11-15)

Primary citation

Pierson, W.E.,Hoffer, E.D.,Keedy, H.E.,Simms, C.L.,Dunham, C.M.,Zaher, H.S.
Uniformity of Peptide Release Is Maintained by Methylation of Release Factors.
Cell Rep, 17:11-18, 2016

PubMed Abstract: Termination of protein synthesis on the ribosome is catalyzed by release factors (RFs), which share a conserved glycine-glycine-glutamine (GGQ) motif. The glutamine residue is methylated in vivo, but a mechanistic understanding of its contribution to hydrolysis is lacking. Here, we show that the modification, apart from increasing the overall rate of termination on all dipeptides, substantially increases the rate of peptide release on a subset of amino acids. In the presence of unmethylated RFs, we measure rates of hydrolysis that are exceptionally slow on proline and glycine residues and approximately two orders of magnitude faster in the presence of the methylated factors. Structures of 70S ribosomes bound to methylated RF1 and RF2 reveal that the glutamine side-chain methylation packs against 23S rRNA nucleotide 2451, stabilizing the GGQ motif and placing the side-chain amide of the glutamine toward tRNA. These data provide a framework for understanding how release factor modifications impact termination.

PubMed: 27681416
DOI: 10.1016/j.celrep.2016.08.085

Experimental method

X-RAY DIFFRACTION (3.09997551079 Å)