Structural basis of tRNA recognition by the widespread OB fold

Aline Umuhire Juru, Rodolfo Ghirlando and Jinwei Zhang ()
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Aline Umuhire Juru: National Institute of Diabetes and Digestive and Kidney Diseases
Rodolfo Ghirlando: National Institute of Diabetes and Digestive and Kidney Diseases
Jinwei Zhang: National Institute of Diabetes and Digestive and Kidney Diseases

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNAIle, which reveals that Trbp recognizes tRNAs solely by capturing their 3′ ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3′ terminal location, and specific sequence of the 3′ CA dinucleotide — a universal feature of mature tRNAs. Arc1p supplements its OB – tRNA 3′ end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.

Date: 2024
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DOI: 10.1038/s41467-024-50730-1

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