SNAP output for PDB entry 6dti [SNAP web server]

PDB-id

6dti; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

X-ray (3.54 Å)

Summary

Structure of the thermus thermophilus 30s ribosomal subunit complexed with an unmodifed anticodon stem loop (asl) of escherichia coli transfer RNA arginine 2 (trnaarg2) bound to an mrna with an cgu-codon in the a-site and paromomycin

Reference

Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy IV FV, Ranganathan SV, Sarachan KL, Agris PF (2020): "A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine." J.Mol.Biol., 432, 913-929. doi: 10.1016/j.jmb.2019.12.016.

Abstract

Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA_Arg isoacceptors. The anticodon stem and loop (ASL) domains of tRNA_Arg1 and tRNA_Arg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I₃₄) and 37 (m₂A₃₇). tRNA_Arg1 is also modified from cytidine to 2-thiocytidine at position 32 (s₂C₃₂). The s₂C₃₂ modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s₂C₃₂ for C₃₂ in the Saccharomyces cerevisiae tRNA_IleIAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s₂C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASL_Arg1ICG and ASL_Arg2ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C_32-A₃₈ cross-loop interaction but failed to fully explain the means by which s₂C₃₂ restricts I₃₄ wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C_32-A₃₈ cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.