The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNA^Phe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end

The crystal structure of the ternary complex of (αβ)₂ heterotetrameric phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus with cognate tRNA^Phe and a nonhydrolyzable phenylalanyl-adenylate analogue (PheOH-AMP) has been determined at 3.1 Å resolution. It reveals conformational changes in tRNA^Phe induced by the PheOH-AMP binding. The single-stranded 3′ end exhibits a hairpin conformation in contrast to the partial unwinding observed previously in the binary PheRS·tRNA ^Phe complex. The CCA end orientation is stabilized by extensive base-specific interactions of A76 and C75 with the protein and by intra-RNA interactions of A73 with adjacent nucleotides. The 4-amino group of the "bulged out" C75 is trapped by two negatively charged residues of the β subunit (Gluβ31 and Aspβ33), highly conserved in eubacterial PheRSs. The position of the A76 base is stabilized by interactions with Hisα212 of motif 2 (universally conserved in PheRSs) and class II-invariant Argα321 of motif 3. Important conformational changes induced by the binding of tRNA^Phe and PheOH-AMP are observed in the catalytic domain: the motif 2 loop and a "helical" loop (residues 139-152 of the α subunit) undergo coordinated displacement; Metα148 of the helical loop adopts a conformation preventing the 2′-OH group of A76 from approaching the α-carbonyl carbon of PheOH-AMP. The unfavorable position of the terminal ribose stems from the absence of the α-carbonyl oxygen in the analogue. Our data suggest that the idiosyncratic feature of PheRS, which aminoacylates the 2′-OH group of the terminal ribose, is dictated by the system-specific topology of the CCA end-binding site.