Translocation of the ribosome

Translocation of the ribosome. This process is catalyzed by EF-G, with the hydrolysis of one molecule of GTP to GDP + Pi. 

The correctly positioned eukaryotic SOS ribosome-Met-tRNAj complex is now ready to begin the task of stepwise addition of amino acids by the in-frame translation of the mRNA. As is the case with initiation, a set of special proteins, termed elongation factors (EFs), are required to carry out this process of chain elongation. The key steps in elongation are entry of each succeeding aminoacyl-tRNA, formation of a peptide bond, and the movement, or translocation, of the ribosome one codon at a time along the mRNA. 

EF2-GTP to EF2-GDP during chain elongation leads to translocation of the ribosome along the mRNA (see Figure... 

The final step of elongation is the translocation of the ribosome a distance of one codon in the 30 direction. This step requires the hydrolysis of another GTP and results in the displacement of the A site into the codon3 position. The dipeptidyl-tRNA stays bound to the mRNA at codon2, but since the ribosome is translocated, this tRNA is now within the P site. This translocation process also creates an empty A site for the next aminoacyl-tRNA and the E site (not shown in Fig. 26.11) now contains the deacylated-tRNA. The bacterial elongation factor EF-G is required for ribosome translocation and it is thought that hydrolysis of GTP results in a conformational change in the ribosome to facilitate the translocation step. This series of three steps is repeated for each amino acid added to the growing polypeptide chain (Fig. 26.13). 

The charging of the tRNA molecule with the aminoacyl moiety requires the hydrolysis of an ATP to an AMP, equivalent to the hydrolysis of two ATPs to two ADPs and phosphates. The entry of the aminoacyl-tRNA into the A site results in the hydrolysis of one GTP to GDP. Translocation of the newly formed pep-tidyl-tRNA in the A site into the P site by EF2 similarly results in hydrolysis of GTP to GDP and phosphate. Thus, the energy requirements for the formation of one peptide bond include the equivalent of the hydrolysis of two ATP molecules to ADP and of two GTP molecules to GDP, or the hydrolysis of four high-energy phosphate bonds. A eukaryotic ribosome can incorporate as many as six amino acids per second prokaryotic ribosomes incorporate as many as 18 per second. Thus, the process of peptide synthesis occurs with great speed and accuracy until a termination codon is reached. 

In order to allow for translocation of the tRNA-mRNA complex, the ribosome will have to undergo conformational changes as well. The contacts described above between the decoding center and the codon-anticodon helix as well as the base pairs between the SOS A and P loops and the tRNA acceptor stems will have... 

Figure 8 EF-G-catalyzed translocation of the tRNA-mRNA complex within the ribosome, (a) Hybrid state formation and intersubunit rotation. Upon peptide bond formation, the ribosome fluctuates between the classical state and a hybrid state. In the classical state, the tRNAs are bound to the A and P site on both the 308 and 508 subunit. In the hybrid state, the anticodons remain in the A and P site on the 308 subunit whereas the acceptor ends move into the P and E site on the 508 subunit, respectively. 8imultaneously to hybrid state formation, the 308 subunit rotates relative to the 508 subunit as shown on the right site, (b) Kinetic mechanism of EF-G-catalyzed translocation. Upon GTP hydrolysis, unlocking occurs through a ribosomal rearrangement. Only subsequently, tRNA and mRNA movement as well as dissociation of the inorganic phosphate from EF-G take place.

Macrolides, lincosamides and streptogramins are protein biosynthesis inhibitors that bind to 50S subunit of the ribosome and inhibit peptidyl tRNA translocation from the A-site to the P-site." Macrolides have a glycosylated 14-, 15- or 16-membered lactone ring structure and are produced by several species of Streptomyces. Lincosamide antibiotics were isolated initially from Streptomyces lincolnensis but later isolated from different species of Streptomcyces. Streptogramins were also isolated from Streptomycesgraminofaciens and subsequently from several different Streptomyces species. There are two structurally different streptogramins, A and B they are bacteriostatic individually and can be bactericidal when combined. 

Elongation Step 3 Translocation In the final step of the elongation cycle, translocation, the ribosome moves one codon toward the 3 end of the mRNA (Fig. 27-25a). This movement shifts the anticodon of the dipeptidyl-tRNA, which is still attached to the second codon of the mRNA, from the A site to the P site, and shifts the de-acylated tRNA from the P site to the E site, from where the tRNA is released into the cytosol. The third codon of the mRNA now lies in the A site and the second codon in the P site. Movement of the ribosome along the mRNA requires EF-G (also known as translocase) and the energy provided by hydrolysis of another molecule of GTP. 

Elongation factor EF-G and translocation. The third step in the elongation sequence on ribosomes (Fig. 29-12, step g) depends upon EF-G, a monomeric GTP-binding protein with a sequence homologous with that of other members of the G protein family. It apparently utilizes the Gibbs energy of hydrolysis of GTP to GDP to drive translocation of the peptidyl-tRNA from the A site to the P site (Fig. 29-12) and of the previously utilized (de-acylated) tRNA to the exit site. 

Steps in bacterial protein synthesis and targets of (1) chloramphenicol (2) macrolides, clindamycin, and type B streptogramins and (3) tetracyclines. The 70S ribosomal mRNA complex is shown with its 50S and 30S subunits. The peptidyl tRNA at the donor site donates the growing peptide chain to the aminoacyl tRNA at the acceptor site in a reaction catalyzed by peptidyl transferase. The tRNA, discharged of its peptide, is released from the donor site to make way for translocation of the newly formed peptidyl tRNA. The acceptor site is then free to be occupied by the next "charged" aminoacyl tRNA. 

One ATP is used for charging of the tRNA, and then one GTP at each of the steps of binding aminoacyl-tRNA to the A site of the ribosome, and translocation. Thus, ignoring initiation, the equivalent of three ATPs are used for each amino acid incorporated. But remember that in amino acid activation, the products are AMP and PP(, the latter being hydrolyzed to Pj to drive the reaction to completion. Thus, the equivalent of four high-energy phosphate bonds are used for each amino acid incorporated. 

Binds to 70S ribosomal 5 OS subunit 23S rRNA inhibits translocation of the peptidyl tRNA from the A site to the P site [antibacterial]... 

---