TRNA binding sites

Several key concepts are worth remembering. GTP is used as an energy source for translation, but ATP is used to form the aminoacyl-tRNA. The ribosome effectively has two kinds of tRNA binding sites. Only tRNAMet can bind to the P (for peptide) site, and this only occurs during the initial formation of the functional ribosome (initiation). All other aminoacyl-tRNAs enter at the A (for amino acid) binding site. After formation of the peptide bond (this doesn t require GTP hydrolysis), the tRNA with the growing peptide attached is moved (translocated) to the other site (this does require GTP hydrolysis). 

We know that there are three tRNA-binding sites that bridge the small and large subunits, two of them bound to the mRNA by anticodon-codon base pairs. These sites are called the A (aminoacyl) and the P (peptidyl) sites. The third site, as we will see later, binds... 

In the 70 S initiation complex, formylme-thionine tRNA is initially located at a binding site known as the peptidyl site (P). A second binding site, the acceptor site (A), is not yet occupied during this phase of translation. Sometimes, a third tRNA binding site is defined as an exit site (E), from which uncharged tRNAs leave the ribosome again (see p. 252 not shown). 

Several sites on the ribosome interact with tRNA (Fig. 4.1) and also are targeted by antibiotics. The peptidyl-tRNA binding site (P-site) of the large subunit binds to the 3 end of peptidyl-tRNA. The aminoacyl-tRNA binding site (A-site) of the... 

Electron microscopic studies of the ribosome at increasingly high resolution provided views of the overall structure and revealed the positions of tRNA-binding sites. Astounding progress on the structure of the ribosome has been made by x-ray crystallographic methods, after the pioneering work by Ada Yonath. The structures of both the 30S and the 50S subunits have been determined at or close to atomic resolution, and the elucidation of the structure of intact 70S... 

Ribosomes Have Three tRNA-Binding Sites That Bridge the 30S and SOS Subunits... 

Figure 29.22. Transfer RNA-Binding Sites. (A) Three tRNA-binding sites are present on the 70S ribosome. They are called the A (for aminoacyl), P (for peptidyl), and E (for exit) sites. Each tRNA molecule contacts both the SOS and the 50S subunit. (B) The tRNA molecules in sites A and P are base paired with mRNA.

Tagging a ribosomal site. Design an affinity-labeling reagent for one of the tRNA binding sites in E. coli ribosomes. 

Ribosomal RNA (rRNA) is a component of the ribosomes, the protein synthesis factories in the cell. rRNA molecules are extremely abundant, making up at least 80 percent of the RNA molecules found in a typical eukaryotic cell. Virtually all ribosomal proteins are in contact with rRNA. Most of the contacts between ribosomal subunits are made between the 16S and 23 S rRNAs such that the interactions involving rRNA are a key part of ribosome function. The environment of the tRNA-binding sites is largely determined by rRNA. The rRNA molecules have several roles in protein synthesis. 16S rRNA plays an active role in the functions of the 308 subunit. It interacts directly with mRNA, with the 508 subunit, and with the anticodons of tRNAs in the P- and A-sites. Peptidyl transferase activity resides exclusively in the 238 rRNA. Finally, the rRNA molecules have a structural role. They fold into three-dimensional shapes that form the scaffold on which the ribosomal proteins assemble. 

The ribosome has two sites for binding tRNA molecules. The first site, called the peptidyl tRNA binding site (P-site), holds the peptidyl tRNA, the growing peptide bound to a tRNA molecule. The second site, called the aminoacyl tRNA... 

Three tRNA binding sites on the 70S ribosome are involved in the process of elongation. Figure 27.22 shows a single round of this cycle, which is repeated until a signal for termination is encountered. The cycle goes as follows ... 

Figure 1.84 Schematic of translation. The mRNA codons are read and converted from nucleoside sequences to protein primary structure by means of cognate aminoacyl-tRNAs. All mRNA codons are translated at a ribosome (prepared from rRNA) that has two cognate aminoacyl-tRNA binding sites P (peptidyl) and A (aminoacyl). All tRNAs are "adaptors" that can bind a particular mRNA codon through their anticodon loop, using Watson-Crick base pairing, and also associate covalently with the appropriate amino acid residue coded for by the corresponding mRNA codon When two cognate aminoacyl-tRNA molecules bind mRNA in P and A sites (a), then both are close enough for peptide link formation to take place with the emergence of a peptide chain (b). As amino acyl tRNA molecules continue to dock sequentially onto mRNA codons (in the direction 5 (c), and amino acid residues continue to be added (W —> C ) (d),...

Ribosomes (Fig. 69.1) contain three tRNA binding sites called E-site, P-site and A-site which are involved in protein synthesis (Chapter 70). 

---