Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 79, Issue 7, Pages 2065-2075Publisher
WILEY
DOI: 10.1002/prot.23026
Keywords
crystal structure; ITC; ATP; tRNA; Archaea; structural genomics; hypothetical protein; Sulfolobus tokodaii
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Funding
- RIKEN Structural Genomics/Proteomics Initiative (RSGI)
- The National Project on Protein Structural and Functional Analyses
- Ministry of Education, Culture, Sports, Science and Technology of Japan
- The Targeted Proteins Research Program (TPRP)
- JSPS (Japan Society for the Promotion of Science)
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The hypermodified nucleoside N-6-threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N-6-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 mu M and 2.6 mM, respectively. We determined the crystal structure of S. tokodaii Sua5, complexed with AMPPNP and L-threonine, at 1.8 angstrom 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 N-6-threonylcarbamoyladenosine.
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