Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP

The hypermodified nucleoside N⁶‐threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N⁶‐threonylcarbamoyl moiety is composed of L ‐threonine and bicarbonate, and its synthesis was genetically shown to require YrdC/Sua5. YrdC/Sua5 binds to tRNA and ATP. In this study, we analyzed the L ‐threonine‐binding mode of Sua5 from the archaeon Sulfolobus tokodaii. Isothermal titration calorimetry measurements revealed that S. tokodaii Sua5 binds L ‐threonine more strongly than L ‐serine and glycine. The Kd values of Sua5 for L ‐threonine and L ‐serine are 9.3 μM and 2.6 mM, respectively. We determined the crystal structure of S. tokodaii Sua5, complexed with AMPPNP and L ‐threonine, at 1.8 Å resolution. The L ‐threonine is bound next to AMPPNP in the same pocket of the N‐terminal domain. Thr118 and two water molecules form hydrogen bonds with AMPPNP in a unique manner for adenine‐specific recognition. The carboxyl group and the side‐chain hydroxyl and methyl groups of L ‐threonine are buried deep in the pocket, whereas the amino group faces AMPPNP. The L ‐threonine is located in a suitable position to react together with ATP for the synthesis of N⁶‐threonylcarbamoyladenosine. Proteins 2011. © 2011 Wiley‐Liss, Inc.