Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP

N⁶-Threonylcarbamoyladenosine (t⁶A) is a modified tRNA base required for accuracy in translation. Qri7 is localized in yeast mitochondria and is involved in t⁶A biosynthesis. In t⁶A biosynthesis, threonylcarbamoyl-adenylate (TCA) is synthesized from threonine, bicarbonate and ATP, and the threonyl-carbamoyl group is transferred to adenine 37 of tRNA by Qri7. Qri7 alone is sufficient to catalyze the second step of the reaction, whereas the Qri7 homologues YgjD (in bacteria) and Kae1 (in archaea and eukaryotes) function as parts of multi-protein complexes. In this study, the crystal structure of Qri7 complexed with AMP (a part of TCA) has been determined at 2.94 Å resolution in a new crystal form. The manner of AMP recognition is similar, with some minor variations, among the Qri7/Kae1/YgjD family proteins. The previously reported dimer formation was also observed in this new crystal form. Furthermore, a comparison with the structure of TobZ, which catalyzes a similar reaction to t⁶A biosynthesis, revealed the presence of a flexible loop that may be involved in tRNA binding.