9J4O

Crystal structure of B. subtilis Leucine tRNA with UAA anticodon

Summary for 9J4O

• Entry DOI: 10.2210/pdb9j4o/pdb
• Descriptor: Leucine tRNA_UAA (89-MER), SPERMINE (2 entities in total)
• Functional Keywords: trna, rna
• Biological source: Bacillus subtilis subsp. subtilis str. 168
• Total number of polymer chains: 1
• Total formula weight: 28951.46

Authors

Kim, J.,Cho, G. (deposition date: 2024-08-09, release date: 2025-07-09)

Primary citation

Cho, G.,Yoo, J.,Shin, K.,Lee, J.,Lim, J.,Kim, J.
Crystal structures of free-state tRNALeu reveal conformational flexibility of Type-II tRNAs.
Rna, 2025

PubMed Abstract: Transfer RNAs (tRNAs) are classified into Type-I and Type-II based on the length of their variable loops, with Type-II characterized by an extended variable loop. While structures of Type-I tRNAs have been well-documented, standalone structures of Type-II tRNAs have not been reported. Here, we present the first crystal structures of two free-state Type-II tRNAs, specifically tRNALeu from Bacillus subtilis and Escherichia coli. Our structures reveal that the B. subtilis tRNALeu anticodon stem-loop (ASL) retains its canonical conformation. The variable loops in both structures are well-defined, displaying a distinctive tetranucleotide loop conformation. Comparisons with Type-I tRNA and biomolecule-bound tRNAs highlight the flexibility of the ASL, variable loop, and terminal CCA residues in Type-II tRNAs, suggesting that this structural plasticity is crucial for their biological interactions and function. These findings provide new insights into the structural dynamics and functional roles of Type-II tRNAs.

PubMed: 40562537
DOI: 10.1261/rna.080596.125

Experimental method

X-RAY DIFFRACTION (2.5 Å)