Structural Aspects of Phenylalanylation and Quality Control in Three Major Forms of Phenylalanyl-tRNA Synthetase

Aminoacyl-tRNA synthetases (aaRSs) are a canonical set of enzymes that specifically attach corresponding amino acids to their cognate transfer RNAs in the cytoplasm, mitochondria, and nucleus. The aaRSs display great differences in primary sequence, subunit size, and quaternary structure. Existence of three types of phenylalanyl-tRNA synthetase (PheRS)—bacterial , eukaryotic/archaeal cytosolic , and mitochondrial —is a prominent example of structural diversity within the aaRSs family. Although archaeal/eukaryotic and bacterial PheRSs share common topology of the core domains and the B3/B4 interface, where editing activity of heterotetrameric PheRSs is localized, the detailed investigation of the three-dimensional structures from three kingdoms revealed significant variations in the local design of their synthetic and editing sites. Moreover, as might be expected from structural data eubacterial, Thermus thermophilus and human cytoplasmic PheRSs acquire different patterns of tRN anticodon recognition. 1. Introduction Aminoacyl-tRNA synthetases are primary actors at the first stage of protein translation, catalyzing the attachment of the correct amino acid to its cognate tRNA in a two-step reaction [1, 2]. At the first step, amino acid is activated by ATP resulting in formation of an enzyme-bound aminoacyl-adenylate. In the second step, the amino acid moiety is transferred onto the -terminal ribose of the cognate tRNA, leading to synthesis of aminoacyl-tRNA. AaRSs vary greatly in amino acid sequences, three-dimensional structures, and subunit organizations. After the three-dimensional structures of four different aaRSs from various sources were determined, analysis of the structures coupled with multiple sequence alignments led to subdivision of the aaRSs family into two different classes (Table 1) [3].It was shown that the active site of class I aaRSs is associated with a classical dinucleotide-binding Rossmann fold, while the active site of class II is formed by an antiparallel β-sheet flanked by helices on both sides. Another discrepancy between the classes is related to the site of amino acid attachment: class I enzymes attach the amino acid substrate to the -OH group of terminal ribose, whereas class II enzymes attach the amino acid to the -OH group (with PheRS being the only exception from this rule). Table 1: Table of division of aaRSs into classes. At the amino acid binding and recognition step, some aaRSs prior to activation face the challenge of discrimination between amino acids with closely similar chemical structures. To ensure a high level