Peptidyl Transferase

Enzymes are a class of biological molecules with the ability to make biochemical reactions in the body faster, i.e. they speed up the rate of reaction. This also helps in the regulation of certain substances in the body, and a relatively key enzyme in the body is peptidyl transferase which is involved in protein synthesis and translation of RNA to proteins.

This article is focused on the concept of peptidyl transferase and its specific course and mechanism in the body as a whole as it provides information on the said enzyme.

What is a Transferase?

A transferase is part of a class of enzymes whose primary function is to catalyze the transfer of a radical/functional group e.g. methyl-, ethyl-, nitro- groups from one substrate to another.

To add a background, enzymes are catalysts for reactions in biological systems. This is because organic reactions are very slow as compared to inorganic ones, and in living systems, this level of speed is not efficient.

The main function of an enzyme is to convert what is working on(the substrate) to what the body needs(the product).

Hence, the use of catalysts(enzymes) increases the speed of reactions occurring in the system. 

Examples of Transferases

Some examples of transferases are:

• D-hexose-6-phosphotransferase also called Hexokinase, which catalyzes the transfer of a phosphoryl group(-PO34) in the first step of glycolysis.
• Serotonin N-transferase
• Glutamate Pyruvate Transferase(Alanine Transaminase)
• Peptidyl Transferase

What is Peptidyl Transferase?

Peptidyl transferase is an example of an aminoacyl transferase that catalyzes the transfer of an amino acid group(called amino acid residue) to a polypeptide chain(substrate) to create a much larger polypeptide chain(product).

Peptidyl transferase is a special type of enzyme as it is formed completely from RNA(ribonucleic acid), a super compressed molecule that contains genetic information and can create new proteins(protein synthesis) from precursors called amino acids.

Peptidyl transferase is located in the large ribosomal subunit, where it catalyzes protein synthesis and peptide bond formation- a step in protein synthesis.

Mechanism of Action of Peptidyl Transferase

Background

Since the ribosome is the site for protein synthesis and peptide transferase catalyzes a step in protein synthesis, we have that the peptidyl transferase enzyme is located in the ribosome.

The ribosome has 3 binding sites where molecules can stay and be worked on; the P site, the A site, and the E site.

The first site is the A site(aminoacyl site). It is the entry point for aminoacyl tRNA bringing the new amino acid chain that is to be added to the growing polypeptide chain. 

The second site is the P site(peptidyl site). It holds the tRNA that is connected to the maturing polypeptide chain until a w stop codon is reached, this causing the peptidyl-tRNA bond found in the P site to be cleared, hence releasing the just produced protein.

The E site(exit site) is the location where the empty tRNA molecule leaves the ribosome after transferring the maturing protein to another tRNA molecule. 

Breakdown of Mechanism of Peptidyl Transferase

Every cycle of peptidyl transferase begins with a tRNA molecule bonded to the I site containing a maturing polypeptide chain(then the aminoacyl tRNA will then bind to the A-site).

The mechanism involves the following steps:

• Nucleophilic attack by the amine of A site to the ester carbon on P site
• The active site of peptide transferase accepts the intermediate formed to produce oxyanion.
• The collapse of the tetrahedral intermediate
• Formation of carbonyl bond{gives rise to loss of leaving group(which is the P site ribose ring)}
• Formation of non-acylated tRNA molecule in the P site 
• Transfer of polypeptide chain to tRNA molecule in A site(via ester to linkages to 3′ -OH groups on tRNA molecule In A site)

Functions of Peptidyl Transferase

Peptidyl transferase has several functions which are:

• Transfer of polypeptide chain from P site to aminoacyl tRNA at A site
• Peptide bond formation in protein synthesis
• Main enzyme for translation (ribosomal translation)

Inhibition of Peptidyl Transferase

Every enzyme has an inhibitor, a compound that reduces its catalytic ability or completely represses its action. 

Peptidyl transferase is no exception as some compounds can inhibit its specific activity. These compounds are:

• Antibiotics

Antibiotics such as capreomycin, spiramycin, and tylosin inhibit peptidyl transferase.

• Drugs

Drugs like tiamulin and valnemulin also inhibit peptidyl transferase

• Toxins

Fungal toxins like the epoxy trichothecenes, bacterial ones like Shiga toxins are examples of toxins that can disrupt peptide transferase activity.

Activators of Peptidyl Transferase

Peptidyl transferase does not have a direct activator. An activator is a compound that enhances the performance of an enzyme or catalyst. 

However, the activity of peptidyl transferase is modulated and under the control of the ribosome via ribosomal RNA(rRNA).

Conclusion

It can be seen that the enzyme; peptidyl transferase is an integral part of the mechanism of the body and without its functioning, the all-important protein synthesis process will be hindered; causing harm to the human system. Hence, the need for this enzyme to be functional in the ribosome is very much emphasized.