Phenylalanyl-tRNA synthetase contains a dispensable RNA-binding domain that contributes to the editing of noncognate aminoacyl-tRNA

Phenylalanyl-tRNA synthetase (PheRS) is a multidomain (alphabeta)2 heterotetrameric protein responsible for synthesizing Phe-tRNA(Phe) during protein synthesis. Previous studies showed that the alpha subunit forms the catalytic core of the enzyme, while the beta subunit contains a number of autonomous structural modules with a wide range of functions including tRNA anticodon binding and editing of the misaminoacylated species Tyr-tRNA(Phe). The B2 domain of the beta subunit is a structural homologue of the EMAPII/OB fold, which has been shown in other systems to contribute to tRNA binding. Structural studies of PheRS indicated that the B2 domain is distant from bound tRNA(Phe), leaving the role of this module in question. On the basis of homology modeling with other EMAPII domain-containing proteins, the 110 amino acid B2 domain was deleted to produce PheRS deltaB2. Full-length PheRS and PheRS deltaB2 showed comparable kinetics for in vitro aminoacylation, and both enzymes complemented a defect in phenylalanylation in vivo. PheRS deltaB2 showed a 2-fold drop compared to full-length PheRS in the catalytic efficiency (kcat/KM) of Tyr-tRNA(Phe) hydrolysis, suggesting a role for the B2 domain in post-transfer editing. A comparison of tRNA binding by full-length PheRS and PheRS deltaB2 indicated that the B2 domain acts as a secondary tRNA-binding site that could contribute to editing by promoting the translocation of mischarged tRNA to the editing site of PheRS. This proposed role for the B2 domain of PheRS is consistent with previous studies, suggesting that the highly conserved EMAPII fold is able to modulate the affinity of tRNA for its primary binding site.