This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1fyp
From Proteopedia
|
EUKARYOTIC DECODING REGION A-SITE RNA-PAROMOMYCIN COMPLEX
Overview
Aminoglycoside antibiotics, including paromomycin, neomycin and, gentamicin, target a region of highly conserved nucleotides in the, decoding region aminoacyl-tRNA site (A site) of 16 S rRNA on the 30 S, subunit. Change of a single nucleotide, A1408 to G, reduces the affinity, of many aminoglycosides for the ribosome; G1408 distinguishes between, prokaryotic and eukaryotic ribosomes. The structures of a prokaryotic, decoding region A-site oligonucleotide free in solution and bound to the, aminoglycosides paromomycin and gentamicin C1a were determined previously., Here, the structure of a eukaryotic decoding region A-site oligonucleotide, bound to paromomycin has been determined using NMR spectroscopy and, compared to the prokaryotic A-site-paromomycin structure. A conformational, change in three adenosine residues of an internal loop, critical for, high-affinity antibiotic binding, was observed in the prokaryotic, RNA-paromomycin complex in comparison to its free form. This, conformational change is not observed in the eukaryotic RNA-paromomycin, complex, disrupting the binding pocket for ring I of the antibiotic. The, lack of the conformational change supports footprinting and titration, calorimetry data that demonstrate approximately 25-50-fold weaker binding, of paromomycin to the eukaryotic decoding-site oligonucleotide. Neomycin, which is much less active against Escherichia coli ribosomes with an, A1408G mutation, binds non-specifically to the oligonucleotide. These, results suggest that eukaryotic ribosomal RNA has a shallow binding pocket, for aminoglycosides, which accommodates only certain antibiotics.
About this Structure
1FYP is a Protein complex structure of sequences from [1] with PAR as ligand. Full crystallographic information is available from OCA.
Reference
Structural origins of aminoglycoside specificity for prokaryotic ribosomes., Lynch SR, Puglisi JD, J Mol Biol. 2001 Mar 9;306(5):1037-58. PMID:11237617
Page seeded by OCA on Sun Nov 25 00:32:18 2007
