2M4Q image
Entry Detail
PDB ID:
2M4Q
Keywords:
Title:
NMR structure of E. coli ribosomela decoding site with apramycin
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2013-02-10
Release Date:
2013-03-20
Method Details:
Experimental Method:
Conformers Calculated:
50
Conformers Submitted:
10
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:RNA (27-MER)
Chain IDs:A (auth: 1)
Chain Length:27
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
The impact of aminoglycosides on the dynamics of translation elongation.
Cell Rep 3 497 508 (2013)
PMID: 23416053 DOI: 10.1016/j.celrep.2013.01.027

Abstact

Inferring antibiotic mechanisms on translation through static structures has been challenging, as biological systems are highly dynamic. Dynamic single-molecule methods are also limited to few simultaneously measurable parameters. We have circumvented these limitations with a multifaceted approach to investigate three structurally distinct aminoglycosides that bind to the aminoacyl-transfer RNA site (A site) in the prokaryotic 30S ribosomal subunit: apramycin, paromomycin, and gentamicin. Using several single-molecule fluorescence measurements combined with structural and biochemical techniques, we observed distinct changes to translational dynamics for each aminoglycoside. While all three drugs effectively inhibit translation elongation, their actions are structurally and mechanistically distinct. Apramycin does not displace A1492 and A1493 at the decoding center, as demonstrated by a solution nuclear magnetic resonance structure, causing only limited miscoding; instead, it primarily blocks translocation. Paromomycin and gentamicin, which displace A1492 and A1493, cause significant miscoding, block intersubunit rotation, and inhibit translocation. Our results show the power of combined dynamics, structural, and biochemical approaches to elucidate the complex mechanisms underlying translation and its inhibition.

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