SNAP output for PDB entry 4dr5 [SNAP web server]

PDB-id

4dr5; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome-antibiotic

Method

X-ray (3.45 Å)

Summary

Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, crystallographically disordered cognate transfer RNA anticodon stem-loop and streptomycin bound

Reference

Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G (2013): "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346.

Abstract

During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues and messenger RNA. Our crystal structures display a significant local distortion of 16S ribosomal RNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate anticodon stem-loop analogue complex, while destabilizing the cognate anticodon stem-loop analogue complex. These data reveal how streptomycin disrupts the recognition of cognate anticodon stem-loop analogues and yet improves recognition of a near-cognate anticodon stem-loop analogue.