8WND

Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with tRNA(Ile) and isoleucine

Summary for 8WND

• Entry DOI: 10.2210/pdb8wnd/pdb
• Descriptor: isoleucine--tRNA ligase, tRNA(Ile), ISOLEUCINE, ... (6 entities in total)
• Functional Keywords: ligaseligase-rna complex, ligase-rna complex, ligase/rna
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 4
• Total formula weight: 299357.26

Authors

Chen, B.,Yi, F.,Zhou, H. (deposition date: 2023-10-05, release date: 2024-10-09, Last modification date: 2025-01-22)

Primary citation

Chen, B.,Yi, F.,Luo, Z.,Lu, F.,Liu, H.,Luo, S.,Gu, Q.,Zhou, H.
The mechanism of discriminative aminoacylation by isoleucyl-tRNA synthetase based on wobble nucleotide recognition.
Nat Commun, 15:10817-10817, 2024

PubMed Abstract: The faithful charging of amino acids to cognate tRNAs by aminoacyl-tRNA synthetases (AARSs) determines the fidelity of protein translation. Isoleucyl-tRNA synthetase (IleRS) distinguishes tRNA from tRNA solely based on the nucleotide at wobble position (N34), and a single substitution at N34 could exchange the aminoacylation specificity between two tRNAs. Here, we report the structural and biochemical mechanism of N34 recognition-based tRNA discrimination by Saccharomyces cerevisiae IleRS (ScIleRS). ScIleRS utilizes a eukaryotic/archaeal-specific arginine as the H-bond donor to recognize the common carbonyl group (H-bond acceptor) of various N34s of tRNA, which induces mutual structural adaptations between ScIleRS and tRNA to achieve a preferable editing state. C34 of unmodified tRNA(CAU) (behaves like tRNA) lacks a relevant H-bond acceptor, which disrupts key H-bonding interactions and structural adaptations and suspends the ScIleRS·tRNA(CAU) complex in an initial non-reactive state. This wobble nucleotide recognition-based structural adaptation provides mechanistic insights into selective tRNA aminoacylation by AARSs.

PubMed: 39738040
DOI: 10.1038/s41467-024-55183-0

Experimental method

X-RAY DIFFRACTION (2.8 Å)