Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
Abstract
The 30S ribosomal subunit has two primary functions in protein synthesis. It discriminates against aminoacyl transfer RNAs that do not match the codon of messenger RNA, thereby ensuring accuracy in translation of the genetic message in a process called decoding. Also, it works with the 50S subunit to move the tRNAs and associated mRNA by precisely one codon, in a process called translocation. Here we describe the functional implications of the high-resolution 30S crystal structure presented in the accompanying paper, and infer details of the interactions between the 30S subunit and its tRNA and mRNA ligands. We also describe the crystal structure of the 30S subunit complexed with the antibiotics paromomycin, streptomycin and spectinomycin, which interfere with decoding and translocation. This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process.
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The observed protections for pactamycin actually belong to the ribosomal E site, not the P site.
“in light of an analysis of the atomic structure of the 30S, the observed protections for this antibiotic actually belong to the E site (Carter et al. 2000”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Carter et al. 2000
The Mg2+ ion was also present in the 30S structure in the absence of tetracycline.
“Interestingly, this Mg2+ ion was also present in the 30S structure in the absence of tetracycline (Carter et al. 2000”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Carter et al. 2000
HygB could alter the balance between ram and restrictive states, as has been suggested for streptomycin.
“indicates that it could also alter the balance between ram and restrictive states as has been suggested for streptomycin (Carter et al. 2000”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Carter et al. 2000
Hygromycin B binds close to the very top of H44, in a region containing the A, P, and E sites for tRNA and the binding site for other aminoglycoside antibiotics.
“It binds close to the very top of H44, in a region that contains the A, P, and E sites for tRNA and also the binding site for other aminoglycoside antibiotics (Carter et al. 2000”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Carter et al. 2000
Hygromycin B binds just above the binding site for paromomycin in H44.
“HygB binds just above the binding site for paromomycin in H44 (Fourmy et al. 1996; Carter et al. 2000”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Carter et al. 2000
The antibiotic tetracycline is located between H34 in the head of the 30S and the modeled A site tRNA, on the other side of the tRNA anticodon stem loop relative to the codon:anticodon interaction.
“The antibiotic is located between H34 in the head of the 30S and the modeled A site tRNA, but on the other side of the tRNA anticodon stem loop relative to the codon:anticodon interaction (Figure 2B) (Carter et al. 2000”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Carter et al. 2000
The tetracycline binding site observed in the U1052G mutant structure is located near the highly conserved 16S central pseudoknot and adjacent to the previously established streptomycin binding site.
“The tetracycline binding site observed in the U1052G mutant structure is located near the highly conserved 16S central pseudoknot and adjacent to the previously established streptomycin binding site (18).”
From Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors (2016) · cites this paper as [18]
Tetracycline binding at the second site has not been previously described.
“Tetracycline binding at this position has not been previously described (17 -20).”
From Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors (2016) · cites this paper as [18]
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- Authors
- Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Wimberly, B. T., & Ramakrishnan, V.
- Affiliations
- MRC Laboratory of Molecular Biology (GB)
- Corresponding author
- Ramakrishnan, V.
- Venue
- Nature
- Published
- 2000-09
- Volume
- 407
- Issue
- 6802
- Pages
- 340-348
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2170243611
- Cited by
- 1,615
- References
- 48
- Citations by year
- 2026: 35 · 2025: 33 · 2024: 36 · 2023: 51 · 2022: 48 · 2021: 50 · 2020: 56 · 2019: 55 · 2018: 45 · 2017: 55 · 2016: 56 · 2015: 51 · 2014: 80 · 2013: 70 · 2012: 43
- FWCI
- 29.03
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- Medical Research Council
- National Institute of General Medical Sciences (F31GM019384)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- 30S ribosomal subunit, ribosome structure, antibiotic binding, paromomycin, streptomycin, spectinomycin, translocation, 16S rRNA, tRNA binding, mRNA binding, translation accuracy
- MeSH terms
- Spectinomycin, Anti-Bacterial Agents, Binding Sites, Genetic Code, Models, Molecular, Nucleic Acid Conformation, Paromomycin, Protein Conformation, Ribosomal Proteins, Ribosomes, RNA, Bacterial, RNA, Messenger, RNA, Ribosomal, RNA, Ribosomal, 16S, RNA, Transfer, Streptomycin, Structure-Activity Relationship, Thermus thermophilus, Crystallography, X-Ray, Molecular Mimicry, Macromolecular Substances
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