Peptidyl site

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... 

The peptidyl site (P site) is the site on the ribosome where (f)met-tRNAj initially binds. After formation of the first peptide bond, the P site is a binding site for the growii peptide chain. 

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). 

Figure 12-2. Formation of the initiation complex for protein synthesis. Several eukaryotic initiation factors (elFs) ensure proper assembly at each step. The initiator Met-tRNA is bound in the peptidyl site of the SOS complex with its anticodon (black stripes) base paired to the AUG start codon (gray box) of the mRNA.

The synthetase consists of the three modules E1, E2, and E3 (for a complete description, see Sec. II. A). Each module is composed of an activation site forming the acyl or aminoacyl adenylate, a carrier domain which is posttranslationally modified with 4 -phosphopantetheine (Sp), and a condensation domain (Cl, C2) or, alternatively, a structurally similar epimerization domain (Ep). Activation of aminoadipate (Aad) leads to an acylated enzyme intermediate, in which Aad is attached to the terminal cysteamine of the cofactor (El-Spl-Aad) [reactions (1) and (2)]. Likewise, activation of cysteine (Cys) leads to cysteinylated module 2 [reactions (3) and (4)]. For the condensation reaction to occur between aminoadipate as donor and cysteine as acceptor, both intermediates are thought to react at the condensation site of module 1 (Cl). Each condensation site is composed, in analogy to ribosomal peptide formation, of an aminoacyl and a peptidyl site. In this case of initiation, the thioester of Aad enters the P-site, while the thioester of Cys enters the A-site. Condensation occurs and leaves the dipeptidyl intermediate Aad-Cys at the carrier protein of the second module [reaction (5)]. The third amino acid valine is activated on module 3, and Val is attached to the carrier protein 3 [reactions (6) and (7)]. Formation of the tripeptide occurs at the second condensation site C2, with the dipeptidyl intermediate entering the P-site and the valiny 1-intermediate the A-site [reaction (8)]. 

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 . 

P-site The peptidyl site on the ribosome to which Met-tRNA is brought to base pair with the mRNA sequence AUG. It is also the site to which the peptidyl RNA is moved in a process known as translocation following the formation of a new peptide bond. 

Chain initiation Initiation requires the smaller ribosomal subunit, an initiation tRNA (with a 5 -CAU-3 anticodon), mRNA with its initiator codon (S -AUG-3 ), and several initiation factors, all of which form the ribosomal initiation complex. The initiation complex is near completion when a tRNA carrying the amino acid methionine hydrogen bonds to the AUG codon on the mRNA. When these components are in place, the larger ribosomal subunit joins the complex in such a way that the initiator met-tRNAjjj j is localized in the P- or peptidyl site (Figure 9-1). The chain initiation phase ends and a second amino acid can be inserted. 

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. 

FIGURE 46-1 Inhibition of bacterial protein synthesis by tetracyclines. Messenger RNA (mRNA) attaches to the 30S subunit of bacterial ribosomal RNA. The P (peptidyl) site of the 50S ribosomal RNA subunit contains the nascent polypeptide chain normally, the aminoacyl tRNA charged with the next amino acid (aa) to be added to the chain moves into the A (acceptor) site, with complementary base pairing between the anticodon sequence of tRNA and the codon sequence of mRNA. Tetracyclines inhibit bacterial protein synthesis by binding to the 30S subunit and blocking tRNA binding to the A site. 

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. 

As shown for streptomycin, the aminoglycosides bind at the 30 S subunit of the ribosome. The formation of the initiation complex is not inhibited. The translocation of the formylmethionine or peptidyl>t-RNA from the acceptor to the peptidyl site is disturbed. The bound t-RNA shifts the ribosome during the translocation from the decoding site to the condensing site and no more aminoacyl-t-RNA is bound. 

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. 

P-site. The peptidyl site contains the tRNA bound to the polypeptide chain. NB The initiating met-tRNA (or formylmet-tRNA in prokaryotes) binds to this site to start assembly of the ribosome and then polypeptide synthesis. 

Each ribosome has two cavities into which tRNA molecules can fit. The initiating fMet-tRNA binds to the P (peptidyl) site and the next aminoacyl-tRNA dictated by the codon following the... 

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