8G6X

Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site meta-aminobenzoic acid charged NH-tRNAPhe

Summary for 8G6X

• Entry DOI: 10.2210/pdb8g6x/pdb
• Related: 8G6W 8G6Y
• EMDB information: 29786 29787 29788 29789 29790 29800 29807
• Descriptor: 23S rRNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (43 entities in total)
• Functional Keywords: ribosome, non-natural monomers, aminobenzoic acids, unnatural monomers
• Biological source: Escherichia coli; More
• Total number of polymer chains: 34
• Total formula weight: 1417971.23

Authors

Majumdar, C.,Cate, J.H.D. (deposition date: 2023-02-16, release date: 2023-03-22, Last modification date: 2023-11-15)

Primary citation

Majumdar, C.,Walker, J.A.,Francis, M.B.,Schepartz, A.,Cate, J.H.D.
Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.
Acs Cent.Sci., 9:1160-1169, 2023

PubMed Abstract: The () ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), aminobenzoic acid (ABZ), and aminobenzoic acid (ABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by ABZ and then ABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

PubMed: 37396857
DOI: 10.1021/acscentsci.3c00153

Experimental method

ELECTRON MICROSCOPY (2.31 Å)