Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs
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Malte Beringer
Abstract
The major enzymatic activity of the ribosome is the catalysis of peptide bond formation. The active site – the peptidyl transferase center – is composed of ribosomal RNA (rRNA), and interactions between rRNA and the reactants, peptidyl-tRNA and aminoacyl-tRNA, are crucial for the reaction to proceed rapidly and efficiently. Here, we describe the influence of rRNA interactions with cytidine residues in A-site substrate analogs (C-puromycin or CC-puromycin), mimicking C74 and C75 of tRNA on the reaction. Base-pairing of C75 with G2553 of 23S rRNA accelerates peptide bond formation, presumably by stabilizing the peptidyl transferase center in its productive conformation. When C74 is also present in the substrate analog, the reaction is slowed down considerably, indicating a slow step in substrate binding to the active site, which limits the reaction rate. The tRNA-rRNA interactions lead to a robust reaction that is insensitive to pH changes or base substitutions in 23S rRNA at the active site of the ribosome.
©2007 by Walter de Gruyter Berlin New York
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Articles in the same Issue
- 25 years of catalytic RNA: looking younger than ever!
- On the occasion of the 25th anniversary of the discovery of catalytic RNA
- An overview of the RNA world – for now
- Group II introns: structure, folding and splicing mechanism
- Expression of protein-coding genes embedded in ribosomal DNA
- Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs
- The spliceosome: a ribozyme at heart?
- A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes
- Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme
- A 2′-methyl or 2′-methylene group at G+1 in precursor tRNA interferes with Mg2+ binding at the enzyme-substrate interface in E-S complexes of E. coli RNase P
- Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism
- Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof
- RNA self-processing towards changed topology and sequence oligomerization
- Plasminogen-dependent internalization of soluble melanotransferrin involves the low-density lipoprotein receptor-related protein and annexin II
- Could the effect of modeled microgravity on osteogenic differentiation of human mesenchymal stem cells be reversed by regulation of signaling pathways?
