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.
Highlights
IntroductionOnly L-amino acids are utilized for protein synthesis
All living cells, from bacteria to human, contain both Land D-amino acids
Only L-amino acids are utilized for protein synthesis
Summary
Only L-amino acids are utilized for protein synthesis The mechanism of this exclusive use of L-amino acids is not yet fully understood. This is especially notable in bacteria whose cytosol contains about a dozen different D-amino acids that are used as a carbon source, signaling molecules, or building blocks for peptidoglycan cell wall synthesis [1,2]. D-amino acids are present in millimolar concentrations, sometimes with the levels of D-isomers exceeding those of their Lisomers (as in the case of D-alanine and D-glutamate) [2,3]. Organisms, from bacteria to higher eukaryotes, utilize only the L-amino acids for protein synthesis despite the presence of D-amino acids in cell cytosol
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