8VU0

Co-crystal structure of Aquifex aeolicus Trbp111 in complex with E. coli tRNA-Ile

Summary for 8VU0

• Entry DOI: 10.2210/pdb8vu0/pdb
• Descriptor: RNA (76-MER), Methionyl-tRNA synthetase beta subunit (3 entities in total)
• Functional Keywords: ob fold, emapii-like domain, trna-binding, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Aquifex aeolicus; More
• Total number of polymer chains: 4
• Total formula weight: 73741.86

Authors

Umuhire Juru, A.,Zhang, J. (deposition date: 2024-01-27, release date: 2024-08-07)

Primary citation

Umuhire Juru, A.,Ghirlando, R.,Zhang, J.
Structural basis of tRNA recognition by the widespread OB fold.
Nat Commun, 15:6385-6385, 2024

PubMed 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 tRNA, 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.

PubMed: 39075051
DOI: 10.1038/s41467-024-50730-1

Experimental method

X-RAY DIFFRACTION (2.64 Å)