Structural Basis of the Initial Binding of tRNA super(Ile Lysidine Synthetase TilS with ATP and L-Lysine)

In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA super(Ile) sub(2) with the lysidine residue at the wobble position. Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA super(Ile lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we determined the crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg) super(2)+, and L-lysine, at 2.5 Aa resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg super(2+. In these initial binding modes, the ATP, Mg) super(2)+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex.