7URM

allo-tRNAUTu1A in the P site of the E. coli ribosome

Summary for 7URM

• Entry DOI: 10.2210/pdb7urm/pdb
• Related: 7URI
• EMDB information: 26714
• Descriptor: allo-tRNAUTU1A (1 entity in total)
• Functional Keywords: trna, selenocysteine, ribosome, rna
• Biological source: metagenome
• Total number of polymer chains: 1
• Total formula weight: 28782.01

Authors

Zhang, J.,Prabhakar, A.,Krahn, N.,Vargas-Rodriguez, O.,Krupkin, M.,Fu, Z.,Acosta-Reyes, F.J.,Ge, X.,Choi, J.,Crnkovic, A.,Ehrenberg, M.,Viani Puglisi, E.,Soll, D.,Puglisi, J. (deposition date: 2022-04-22, release date: 2022-08-10, Last modification date: 2024-06-12)

Primary citation

Prabhakar, A.,Krahn, N.,Zhang, J.,Vargas-Rodriguez, O.,Krupkin, M.,Fu, Z.,Acosta-Reyes, F.J.,Ge, X.,Choi, J.,Crnkovic, A.,Ehrenberg, M.,Puglisi, E.V.,Soll, D.,Puglisi, J.
Uncovering translation roadblocks during the development of a synthetic tRNA.
Nucleic Acids Res., 50:10201-10211, 2022

PubMed Abstract: Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNAUTu1, a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNAUTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.

PubMed: 35882385
DOI: 10.1093/nar/gkac576

Experimental method

ELECTRON MICROSCOPY (3 Å)