title: Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP.
abstract: 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 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 N(6)-threonylcarbamoyladenosine.
authors.affiliation: RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Kuratani
authors.forename: Takuma
authors.initials: T
authors.lastname: Kasai
authors.forename: Ryogo
authors.initials: R
authors.lastname: Akasaka
authors.forename: Kyoko
authors.initials: K
authors.lastname: Higashijima
authors.forename: Takaho
authors.initials: T
authors.lastname: Terada
authors.forename: Takanori
authors.initials: T
authors.lastname: Kigawa
authors.forename: Akeo
authors.initials: A
authors.lastname: Shinkai
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Bessho
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000266:Adenylyl Imidodiphosphate / Q000737:chemistry* / Q000378:metabolism; D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism; D002151:Calorimetry; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D011485:Protein Binding; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D016944:Sulfolobus / Q000737:chemistry*; D013912:Threonine / Q000737:chemistry* / Q000378:metabolism; D014961:X-Ray Diffraction
chemical_list: D019843:Archaeal Proteins; D016601:RNA-Binding Proteins; D000266:Adenylyl Imidodiphosphate; D013912:Threonine