PMID:14661949
| Citation |
Noah, JW, Shapkina, TG, Nanda, K, Huggins, W and Wollenzien, P (2003) Conformational change in the 16S rRNA in the Escherichia coli 70S ribosome induced by P/P- and P/E-site tRNAPhe binding. Biochemistry 42:14386-96 |
|---|---|
| Abstract |
The effects of P/P- and P/E-site tRNA(Phe) binding on the 16S rRNA structure in the Escherichia coli 70S ribosome were investigated using UV cross-linking. The identity and frequency of 16S rRNA intramolecular cross-links were determined in the presence of deacyl-tRNA(Phe) or N-acetyl-Phe-tRNA(Phe) using poly(U) or an mRNA analogue containing a single Phe codon. For N-acetyl-Phe-tRNA(Phe) with either poly(U) or the mRNA analogue, the frequency of an intramolecular cross-link C967 x C1400 in the 16S rRNA was decreased in proportion to the binding stoichiometry of the tRNA. A proportional effect was true also for deacyl-tRNA(Phe) with poly(U), but the decrease in the C967 x C1400 frequency was less than the tRNA binding stoichiometry with the mRNA analogue. The inhibition of the C967 x C1400 cross-link was similar in buffers with, or without, polyamines. The exclusive participation of C967 with C1400 in the cross-link was confirmed by RNA sequencing. One intermolecular cross-link, 16S rRNA (C1400) to tRNA(Phe)(U33), was made with either poly(U) or the mRNA analogue. These results indicate a limited structural change in the small subunit around C967 and C1400 during tRNA P-site binding sensitive to the type of mRNA that is used. The absence of the C967 x C1400 cross-link in 70S ribosome complexes with tRNA is consistent with the 30S and 70S crystal structures, which contain tRNA or tRNA analogues; the occurrence of the cross-link indicates an alternative arrangement in this region in empty ribosomes. |
| Links |
PubMed Online version:10.1021/bi035369q |
| Keywords |
Acetylation/radiation effects; Binding Sites/radiation effects; Cytosine/chemistry; Cytosine/radiation effects; Escherichia coli/chemistry; Escherichia coli/genetics; Escherichia coli/radiation effects; Nucleic Acid Conformation/radiation effects; Peptide Chain Elongation, Translational/genetics; Peptide Chain Elongation, Translational/radiation effects; Photochemistry; Poly U/chemistry; Poly U/genetics; RNA, Bacterial/chemistry; RNA, Bacterial/genetics; RNA, Bacterial/radiation effects; RNA, Messenger/chemistry; RNA, Messenger/genetics; RNA, Messenger/radiation effects; RNA, Ribosomal, 16S/chemistry; RNA, Ribosomal, 16S/genetics; RNA, Ribosomal, 16S/radiation effects; RNA, Transfer, Phe/chemistry; RNA, Transfer, Phe/genetics; RNA, Transfer, Phe/radiation effects; Ribosomes/chemistry; Ribosomes/genetics; Ribosomes/radiation effects; Transcription, Genetic/radiation effects; Ultraviolet Rays |
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