Function and mechanism of Peptidyltransferase

Working of Peptidyltransferase
Peptidyltransferase center (PTC) is the point where peptide formation occurs. It is located on the 50S subunit of the ribosome and is purely composed of RNA (ribozyme). The chemistry behind the peptide bond formation is as follows:

Step 1: Amino group is deprotonated

Step 2: Tetrahedral intermediate with zwitterion is formed as a result of a nucleophilic attack.

Step 3: Generation of negatively charged intermediate with the second deprotonation.

Step 4: Formation of the product followed by protonation of oxygen leaving the group.

The following two points can explain the mechanism of peptide bond formation:

General acid-base catalysis: It facilitates the activation of the weak nucleophile (NH3+) and stabilizes the low leaving group (O-). At A site, aminoacylated tRNA is attached to initiate the peptide bond formation.

Substrate positioning: Ribosome selects its substrate, i.e., aminoacyl-tRNA, rapidly and accurately. It then starts the catalysis to initiate the peptide bond formation from incoming amino acids. By lowering the activation energy of the reaction, the ribosome accelerates the construction of a peptide bond owing to the positioning of two substrates: allowing water to come at the active site and providing an electrostatic network to stabilize the intermediates formed during the reaction. Once the two substrates come near one another in the correct orientation, peptide bind formation takes place.

In a prokaryotic organism, 23S component of 50S ribosomal unit contains the peptidyltransferase activity, lying at the A- and O- site of the tRNAs. In the eukaryotic organisms, the 28S component of the 60S ribosomal subunit has the peptidyltransferase activity that also acts as a ribozyme.

Function and mechanism of Peptidyltransferase
Peptidyltransferase functions by speeding the rate of reaction followed by the lowering in activation energy. It provides the proper orientation of the reactants to form products. The enzyme does so by bringing the reactants close together to increase the collision resulting in the product formation. It also helps in getting the substrate in proper orientation, hence increasing the probability and assuring the mechanism to take place, leading to the formation of the desired product.

Mechanism of action of peptidyltransferase can be explained stepwise as follows:

The nucleophilic attack is triggered by the amino acid present at the A site on the ester carbon located on the P site of the tRNA.

Tetrahedral intermediate is created as a result of the nucleophilic attack.

Water residue is present in the active site of the tetrahedral intermediate.

The formation of tetrahedral intermediate gives rise to oxyanion with negative charge owing to the extra electron present on the oxygen.

This gives hydrogen of the water an extra positive charge that helps in stabilizing the tetrahedral intermediate consisting of oxyanion.

Tetrahedral intermediate collapses, leading to the reformation of carbonyl bond.

This results in the loss of ribose ring present at the P site of the tRNA (leaving group).

When this leaving group is released, the proton is taken out of the water. This further abstracts the proton included in the amine group of amino acid.

In the end, non-acylatedtRNAremains at the P site and the growing chain of the peptide, including the extra amino acid remains attached to the 3’ OH group at the A site of the tRNA with the ester linkage.