6N9E

Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic CC-Pmn and bound to mRNA and P-site tRNA at 3.7A resolution

This is a non-PDB format compatible entry.

Summary for 6N9E

• Entry DOI: 10.2210/pdb6n9e/pdb
• Descriptor: 23S Ribosomal RNA, 50S Ribosomal Protein L14, 50S Ribosomal Protein L15, ... (59 entities in total)
• Functional Keywords: d-amino acids, ribosome structure, peptidyl transferase center, expanded genetic code, ribosome engineering, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 110
• Total formula weight: 4434074.68

Authors

Melnikov, S.V.,Khabibullina, N.F.,Mairhofer, E.,Vargas-Rodriguez, O.,Reynolds, N.M.,Micura, R.,Soll, D.,Polikanov, Y.S. (deposition date: 2018-12-03, release date: 2018-12-12, Last modification date: 2023-11-15)

Primary citation

Melnikov, S.V.,Khabibullina, N.F.,Mairhofer, E.,Vargas-Rodriguez, O.,Reynolds, N.M.,Micura, R.,Soll, D.,Polikanov, Y.S.
Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.
Nucleic Acids Res., 47:2089-2100, 2019

PubMed Abstract: During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.

PubMed: 30520988
DOI: 10.1093/nar/gky1211

Experimental method

X-RAY DIFFRACTION (3.7 Å)