Structure of the A Site of Escherichia coli 16 S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic
Abstract
Aminoglycoside antibiotics that bind to 30 S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation. The aminoglycoside antibiotic paromomycin binds specifically to an RNA oligonucleotide that contains the 30 S subunit A site, and the solution structure of the RNA-paromomycin complex was determined by nuclear magnetic resonance spectroscopy. The antibiotic binds in the major groove of the model A-site RNA within a pocket created by an A-A base pair and a single bulged adenine. Specific interactions occur between aminoglycoside chemical groups important for antibiotic activity and conserved nucleotides in the RNA. The structure explains binding of diverse aminoglycosides to the ribosome, their specific activity against prokaryotic organisms, and various resistance mechanisms, and provides insight into ribosome function.
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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 Fourmy et al. 1996
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Recognition of Cognate Transfer RNA by the 30 <i>S</i> Ribosomal Subunit
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“In addition, the UV-induced 20 A˚ wide and 7 A˚ deep and is formed by an irregular minor grove of H34 (RNA residues 1196–1200:1053– cross-link between C1402 and C1501, both of which are located in H44, increases in intensity upon Tc binding 1056) in combination with residues 964–967 from the H31 stem-loop.”
BackgroundInfluentialSelection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
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tRNA selection and kinetic proofreading in translation
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- Authors
- Fourmy, D., Recht, M. I., Blanchard, S. C., & Puglisi, J. D.
- Affiliations
- University of California, Santa Cruz (US)
- Corresponding author
- Puglisi, Joseph D.
- Venue
- Science
- Published
- 1996-11-22
- Volume
- 274
- Issue
- 5291
- Pages
- 1367-1371
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W1965252702
- Cited by
- 829
- References
- 0
- Citations by year
- 2026: 11 · 2025: 12 · 2024: 11 · 2023: 23 · 2022: 17 · 2021: 17 · 2020: 32 · 2019: 18 · 2018: 13 · 2017: 13 · 2016: 14 · 2015: 20 · 2014: 30 · 2013: 24 · 2012: 15
- FWCI
- 15.52
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM51266-01A1, R01GM051266)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- aminoglycosides, paromomycin, 30S ribosomal subunit, ribosomal A site, 16S rRNA, antibiotic binding sites, major groove binding, codon misreading, antibiotic resistance, Escherichia coli ribosome
- MeSH terms
- Anti-Bacterial Agents, Base Composition, Binding Sites, Escherichia coli, Hydrogen Bonding, Methylation, Models, Molecular, Magnetic Resonance Spectroscopy, Nucleic Acid Conformation, Oligoribonucleotides, Paromomycin, Ribosomes, RNA, Bacterial, RNA, Ribosomal, 16S
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