Aminoacyl site

CrPV), intergenic region CGU codon placed in the aminoacyl site of the small ribosomal subunit... 

The aminoacyl site (A site) binds each new incoming tRNA molecule carrying an activated amino acid. 

The next aminoacyl-tRNA (Figure 14.5 shows a tRNA specific for alanine) is also bound via a codon (GCG)-anticodon (CGC) interaction and is positioned at an adjacent A (for aminoacyl) site on the ribosome. This allows peptide bond formation to... 

To complete the initiation process, the 50S ribosomal subunit binds to the 3 OS-mRNA complex, with the subsequent hydrolysis of GTP and the release of IF-2 and IF-3 from the 70S ribosomal complex (Fig. 23-3). At this point, the aminoacyl site (A site) of the ribosome is ready to accept the incoming aminoacyl tRNA specified by the codon that occupies this site. 

The ribosome includes three sites for tRNA binding called the A (aminoacyl) site, the P (peptidyl) site, and the E (exit) site. With a tRNA attached to the growing peptide chain in the P site, an aminoacyl-tRNA binds to the A site. A peptide bond is formed when the amino group of the aminoacyl-tRNA nucleophically attacks the ester carbonyl group of the peptidyl-tRNA. On peptide-bond formation, the tRNAs and mRNA must be translocated for the next cycle to begin. The deacylated tRNA moves to the E site and then leaves the ribosome, and the peptidyl-tRNA moves from the A site into the P site. 

Erythromycin acts by binding to the 50S subunit by an unknown mechanism. It works in the same way as chloramphenicol by inhibiting translocation, where the elongated peptide chain attached to tRNA is shifted back from the aminoacyl site to the peptidyl site. Erythromycin was used against penicillin-resistant staphylococci, but newer penicillins are now used for these infections. It is, however, the drug of choice against legionnaires disease . 

Initiation. Translation begins with initiation, when the small ribosomal subunit binds an mRNA. The anticodon of a specific tRNA, referred to as an initiator tRNA, then base pairs with the initiation codon AUG. Initiation ends as the large ribosomal subunit combines with the small subunit. There are two sites on the complete ribosome for codon-anticodon interactions the P (peptidyl) site (now occupied by the enitiator tRNA) and the A (aminoacyl) site. In both prokaryotes and eukaryotes, mRNAs are read simultaneously by numerous ribosomes. An mRNA with several ribosomes bound to it is referred to as a polysome. In actively growing prokaryotes, for example, the ribosomes attached to an mRNA molecule may be separated from each other by as few as 80 nucleotides. 

It is usually accepted that the 16-membered-ring macrolides inhibit peptidyltransferase activity [79, 88, 89], because they inhibit puromycin reaction although poorly. The reaction is used as an assay system for peptidyltransferase activity, because puromycin characteristically interrupts peptide bond formation by virtue of its structural similarity to the 3 end of aminoacyl-tRNA. Puromycin enters the A site (the so-called aminoacyl site) on the ribosome and is incorporated into either a nascent polypeptide or into A-acylaminoacylate, consequently causing premature release of puromycinyl polypeptide or A-acylaminoacyl-puromycin from the ribosome. 

Fig. 15.8. Initiation of protein synthesis. P site = peptidyl site on the ribosome A site = aminoacyl site on the ribosome (The A and P sites or portions of them are indicated by dashed lines) elF = eukaryotic initiation factor.

The A site and the P site on the ribosome are both binding sites for charged tRNAs taking part in protein synthesis. The P (peptidyl) site binds a tRNA to which the growing polypeptide chain is bonded. The A (aminoacyl) site binds to an aminoacyl tRNA. The amino acid moiety is the next one added to the nascent protein. The E (exit) site binds the uncharged tRNA until it is released from the ribosome. 

The binding site of aminoglycosides was ultimately discovered to be the 16S rRNA aminoacyl site (A-site) of the small ribosomal subunit (30S) in prokaryotic bacteria.Studies in the 1980s largely relied on enzymatic footprinting, but advances in NMR and crystallographic techniques have vastly widened the views. As a result of structural elucidations of the complexes, both in solution and in crystal form, there is a much clearer picture of the aminoglycoside-RNA interaction. 

A second site, called the A site (aminoacyl site), is located on the mRNA-ribosome complex next to the P site. The A site is where an incoming tRNA carrying the next amino acid will bond. Each of the tRNA molecules representing the 20 amino acids can fiy to fit the A site, but only the one with the correct anticodon that is complementary to the next codon on the mRNA will fit properly. 

The A site (aminoacyl site) is where an incoming tRNA carrying the next amino acid will bond. The P site (peptidyl site) is where the tRNA carrying the peptide chain is located. 

Sites Studied. Interactions of tRNA with the ribosome can be broadly classified into two types, (a) Interactions with the peptidyltransferase center of the 50 S ribosomal subunit involving the 3 terminus of peptidyl-or aminoacyl-tRNA occupying, respectively, the donor (peptidyl) or acceptor (aminoacyl) site of the catalytic center, (b) Interactions likely to involve internal parts of the tRNA molecule and designed to align and stabilize the binding of cognate tRNAs to the ribosome. 

Fig. 2.1. Peptide bond formation in the biological system. The entire process takes place on the ribosome and involves two binding sites, the P (peptidyl) and A (aminoacyl) sites. The reaction is catalyzed by the enzyme peptidyl transferase. It is the message carried by mRNA (which in turn is dictated by the genetic material DNA) which determines by specific interactions as to which aminoacyl-tRNA will bind at the P and...

Attention should be given to the similarity between solid phase technology and the biological synthesis of proteins. In both cases, an amino acid is attached via the carboxylate function to a large macromolecular surface upon which the sequential addition of other amino acids and peptide bond formation occurs. In one case, the polymer, like the tRNA molecule at the peptidyl site, is the leaving group, while in the other case, the polymer, like the tRNA molecule at the aminoacyl site, remains bound to the chain after formation... 

---