Abstract
The essential process of protein biosynthesis in the cell often gets stalled due to the premature abortion of the translation process and generates a byproduct of peptidyl-tRNA molecules. This defect is corrected by peptidyl-tRNA hydrolase (Pth) by hydrolyzing peptidyl-tRNA to yield tRNA and peptides. In order to understand the mechanism of catalytic action and detailed stereochemical features of the substrate binding site, the structure of Pth has been determined at 1.00 A resolution. The Pth enzyme from Acinetobacter baumannii (AbPth) was cloned, expressed, purified and crystallized. The structure was refined to Rcryst and Rfree values of 0.145 and 0.157 respectively. The electron densities were observed for many hydrogen atoms in the structure. In AbPth, the residues, Asn12, His22, Asn70, Asp95 and Asn116 are involved in the catalytic process. The structure determination revealed that His22 Nᵟ1 forms a hydrogen bond with Asp95 Oᵟ2 while His22 Ne2 is hydrogen bonded to Asn116 Nᵟ2. In this case, the side chain of Asn116 adopts a conformation with value of 65°. Upon ligand binding, Asn116 adopts a different conformation with value of -70⁰. In the present structure, the conformation of Tyr68 is observed in the disallowed region of Ramachandran’s plot with φ, ѱ values of 80⁰, 150⁰. However, it is observed that Tyr68 adopts both disallowed and allowed conformations in Pth enzymes indicating a structural flexibility. The structure determination also revealed multiple conformations of the side chains of a number of amino acid residues.
Highlights
Petidyl-tRNA hydrolase (Pth, EC 3.1.1.29) catalyzes the hydrolysis of peptidyl-tRNA molecules for separating the peptide and tRNA components
It ensures the continuous supply of required raw material of tRNA and amino acids so that the process of protein biosynthesis continues without disruptions
The structure of AbPth consists of 196 residues from the amino acid sequence of Gly-2 - Ser-1 - His- 0 - Met1 to Ala193 (Figure 3) in which the first three residues are from the signal peptide
Summary
Petidyl-tRNA hydrolase (Pth, EC 3.1.1.29) catalyzes the hydrolysis of peptidyl-tRNA molecules for separating the peptide and tRNA components. The peptidyl-tRNA molecules are produced due to a prematurely terminated translation process during protein biosynthesis [1,2,3,4] This undesirable byproduct results in the loss of tRNA and amino acids which adversely affects the process of protein biosynthesis eventually leading to cell death [5,6,7,8]. The stalled process of protein biosynthesis in the cell is restored by Pth enzyme which is an esterase and cleaves the peptidyltRNA molecule at the ester bond between tRNA and peptide component. It ensures the continuous supply of required raw material of tRNA and amino acids so that the process of protein biosynthesis continues without disruptions. The role of Pth enzyme is essential in the regulation of protein biosynthesis in the cell
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