Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue

Abstract

The crystal structures of Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) complexed with phenylalanine and phenylalaninyl-adenylate (PheOH-AMP), the synthetic analogue of phenylalanyl-adenylate, have been determined at 2.7 Å and 2.5 Å resolution, respectively. Both Phe and PheOH-AMP are engulfed in the active site cleft of the catalytic α-subunit of PheRS, and neither makes contact with the PheRS β-subunit. The conformations and binding of Phe are almost identical in both complexes. The recognition of Phe by PheRS is achieved through a mixture of multiple van der Waals interactions and hydrogen bonds. The side-chain of the Phe substrate is sandwiched between the hydrophobic side-chains of Pheα258 and Pheα260 on one side, and the main-chain atoms of the two adjacent β-strands on the other. The side-chains of Valα261 and Alaα314 form the back wall of the amino acid binding pocket. In addition, PheRS residues (Trpα149, Serα180, Hisα178, Argα204, Glnα218, and Gluα220) form a total of seven hydrogen bonds with the main-chain atoms of Phe. The conformation of PheOH-AMP and the network of interactions of its AMP moiety with PheRS are reminiscent of the other class II synthetases. The structural similarity between PheRS and histidyl-tRNA synthetase extends to the amino acid binding site, which is normally unique for each enzyme. The complex structures suggest that the PheRS β-subunit may affect the first step of the reaction (formation of phenylalanyl-adenylate) through the metal-mediated conserved α/β-subunit interface. The modeling of tyrosine in the active site of PheRS revealed no apparent close contacts between tyrosine and the PheRS residues. This result implies that the proofreading mechanism against activated tyrosine, rather than direct recognition, may play the major role in the PheRS specificity.