Crystal Structure of Peptidyl-tRNA Hydrolase from <i>Acinetobacter baumannii</i> at 1.00 Å Resolution

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 Å resolution. The Pth enzyme from Acinetobacter baumannii (AbPth) was cloned, expressed, purified and crystallized. The structure was refined to R cryst and R free 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 Nᵟ 1 forms a hydrogen bond with Asp95 Oᵟ 2 while His22 N ε2 is hydrogen bonded to Asn116 Nᵟ 2 . In this case, the side chain of Asn116 adopts a conformation with χ value of 65°. Upon ligand binding, Asn116 adopts a different conformation with χ 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.