Crystal structures of free-state tRNA^Leu reveal conformational flexibility of type-II tRNAs

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 tRNA^Leu from Bacillus subtilis and Escherichia coli. Our structures reveal that the B. subtilis tRNA^Leu 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.