6UO1

Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA (containing pseudouridine at the first position of the codon) and deacylated A-, P-, and E-site tRNAs at 2.95A resolution

This is a non-PDB format compatible entry.

Summary for 6UO1

• Entry DOI: 10.2210/pdb6uo1/pdb
• Descriptor: 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (59 entities in total)
• Functional Keywords: pseudouridine, mrna, modification, ribosome, translation, peptidyl transferase center, trna accommodation
• Biological source: Thermus thermophilus HB8; More
• Total number of polymer chains: 112
• Total formula weight: 4537656.70

Authors

Batool, Z.,Dobosz-Bartoszek, M.,Polikanov, Y.S. (deposition date: 2019-10-14, release date: 2019-11-27, Last modification date: 2025-03-19)

Primary citation

Eyler, D.E.,Franco, M.K.,Batool, Z.,Wu, M.Z.,Dubuke, M.L.,Dobosz-Bartoszek, M.,Jones, J.D.,Polikanov, Y.S.,Roy, B.,Koutmou, K.S.
Pseudouridinylation of mRNA coding sequences alters translation.
Proc.Natl.Acad.Sci.USA, 116:23068-23074, 2019

PubMed Abstract: Chemical modifications of RNAs have long been established as key modulators of nonprotein-coding RNA structure and function in cells. There is a growing appreciation that messenger RNA (mRNA) sequences responsible for directing protein synthesis can also be posttranscriptionally modified. The enzymatic incorporation of mRNA modifications has many potential outcomes, including changing mRNA stability, protein recruitment, and translation. We tested how one of the most common modifications present in mRNA coding regions, pseudouridine (Ψ), impacts protein synthesis using a fully reconstituted bacterial translation system and human cells. Our work reveals that replacing a single uridine nucleotide with Ψ in an mRNA codon impedes amino acid addition and EF-Tu GTPase activation. A crystal structure of the 70S ribosome with a tRNA bound to a ΨUU codon in the A site supports these findings. We also find that the presence of Ψ can promote the low-level synthesis of multiple peptide products from a single mRNA sequence in the reconstituted translation system as well as human cells, and increases the rate of near-cognate Val-tRNA reacting on a ΨUU codon. The vast majority of Ψ moieties in mRNAs are found in coding regions, and our study suggests that one consequence of the ribosome encountering Ψ can be to modestly alter both translation speed and mRNA decoding.

PubMed: 31672910
DOI: 10.1073/pnas.1821754116

Experimental method

X-RAY DIFFRACTION (2.95 Å)