PMID:9873002: Difference between revisions
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!align=left |Citation | |||
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'''Uchiumi, T, Sato, N, Wada, A and Hachimori, A''' (1999) Interaction of the sarcin/ricin domain of 23 S ribosomal RNA with proteins L3 and L6. ''J. Biol. Chem.'' '''274''':681-6 | |||
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!align=left |Abstract | |||
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We investigated interaction of an RNA domain covering the target site of alpha-sarcin and ricin (sarcin/ricin domain) of Escherichia coli 23 S rRNA with ribosomal proteins. RNA fragments comprising residues 2630-2788 (Tox-1) and residues 2640-2774 (Tox-2) of 23 S rRNA were transcribed in vitro and used to analyze the binding proteins by gel shift and filter binding. Protein L6 bound to both Tox-1 (Kd: 0.31 microM) and Tox-2 (Kd: 0.18 microM), and L3 bound only to Tox-1 (Kd: 0.069 microM) in a solution containing 10 mM MgCl2 and 175 mM KCl at 0 degreesC. Footprinting studies were performed using the chemical probe dimethyl sulfate on full-length 23 S rRNA. Binding of L6 protected a single base, A-2757, and strongly enhanced reactivity of C-2752. A direct role of A-2757 in the L6 binding was verified by site-directed mutagenesis; replacements of A-2757 with G and C impaired the L6 binding. On the other hand, binding of L3 protected A-2632, A-2634, A-2635, A-2675, A-2726, A-2733, A-2749, and A-2750. Interestingly, binding of L6 and L3 together protected additional bases A-2657, A-2662, C-2666, and C-2667 in the sarcin/ricin loop, in addition to A-2740, A-2741, A-2748, A-2753, A-2764, A-2765, and A-2766 in the other stem-loop. This appears to be due to cooperative interaction of L3 and L6 with the RNA. The results are discussed with respect to conformational modulation of the sarcin/ricin domain by the protein binding. | |||
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9873002 PubMed] | |||
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| | !align=left |Keywords | ||
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|- | Base Sequence; Binding Sites; Endoribonucleases/metabolism; Fungal Proteins; Molecular Sequence Data; Nucleic Acid Conformation; Protein Binding; RNA, Ribosomal, 23S/chemistry; RNA, Ribosomal, 23S/metabolism; Ribosomal Proteins/metabolism; Ricin/metabolism | ||
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==Significance {{HelpIcon|Help:Literature}} == | ==Significance {{HelpIcon|Help:Literature}} == | ||
{{LitSignificance}} | {{LitSignificance}} | ||
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==Annotations {{HelpIcon|Help:Literature}}== | ==Annotations {{HelpIcon|Help:Literature}}== | ||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} == | ==EcoliWiki Links {{HelpIcon|Help:Literature}} == | ||
Latest revision as of 05:06, 15 September 2013
| Citation |
Uchiumi, T, Sato, N, Wada, A and Hachimori, A (1999) Interaction of the sarcin/ricin domain of 23 S ribosomal RNA with proteins L3 and L6. J. Biol. Chem. 274:681-6 |
|---|---|
| Abstract |
We investigated interaction of an RNA domain covering the target site of alpha-sarcin and ricin (sarcin/ricin domain) of Escherichia coli 23 S rRNA with ribosomal proteins. RNA fragments comprising residues 2630-2788 (Tox-1) and residues 2640-2774 (Tox-2) of 23 S rRNA were transcribed in vitro and used to analyze the binding proteins by gel shift and filter binding. Protein L6 bound to both Tox-1 (Kd: 0.31 microM) and Tox-2 (Kd: 0.18 microM), and L3 bound only to Tox-1 (Kd: 0.069 microM) in a solution containing 10 mM MgCl2 and 175 mM KCl at 0 degreesC. Footprinting studies were performed using the chemical probe dimethyl sulfate on full-length 23 S rRNA. Binding of L6 protected a single base, A-2757, and strongly enhanced reactivity of C-2752. A direct role of A-2757 in the L6 binding was verified by site-directed mutagenesis; replacements of A-2757 with G and C impaired the L6 binding. On the other hand, binding of L3 protected A-2632, A-2634, A-2635, A-2675, A-2726, A-2733, A-2749, and A-2750. Interestingly, binding of L6 and L3 together protected additional bases A-2657, A-2662, C-2666, and C-2667 in the sarcin/ricin loop, in addition to A-2740, A-2741, A-2748, A-2753, A-2764, A-2765, and A-2766 in the other stem-loop. This appears to be due to cooperative interaction of L3 and L6 with the RNA. The results are discussed with respect to conformational modulation of the sarcin/ricin domain by the protein binding. |
| Links | |
| Keywords |
Base Sequence; Binding Sites; Endoribonucleases/metabolism; Fungal Proteins; Molecular Sequence Data; Nucleic Acid Conformation; Protein Binding; RNA, Ribosomal, 23S/chemistry; RNA, Ribosomal, 23S/metabolism; Ribosomal Proteins/metabolism; Ricin/metabolism |
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