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| {{STRUCTURE_1fyp| PDB=1fyp | SCENE= }} | | {{STRUCTURE_1fyp| PDB=1fyp | SCENE= }} |
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| '''EUKARYOTIC DECODING REGION A-SITE RNA-PAROMOMYCIN COMPLEX'''
| | ===EUKARYOTIC DECODING REGION A-SITE RNA-PAROMOMYCIN COMPLEX=== |
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| ==Overview==
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| 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.
| | The line below this paragraph, {{ABSTRACT_PUBMED_11237617}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 11237617 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_11237617}} |
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| ==About this Structure== | | ==About this Structure== |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FYP OCA]. | | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FYP OCA]. |
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| ==Reference== | | ==Reference== |
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| [[Category: Rna-paromomycin complex]] | | [[Category: Rna-paromomycin complex]] |
| [[Category: Stem-internal loop-stem-tetraloop]] | | [[Category: Stem-internal loop-stem-tetraloop]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 16:54:59 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 04:08:31 2008'' |
