title: Structure of a tRNA-dependent kinase essential for selenocysteine decoding.
abstract: Compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (Sec), the 21(st) natural amino acid (aa). An essential RNA-dependent kinase, O-phosphoseryl-tRNA(Sec) kinase (PSTK), converts seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), the immediate precursor of selenocysteinyl-tRNA(Sec). The sequence of Methanocaldococcus jannaschii PSTK (MjPSTK) suggests an N-terminal kinase domain (177 aa) followed by a presumed tRNA binding region (75 aa). The structures of MjPSTK complexed with ADP and AMPPNP revealed that this enzyme belongs to the P-loop kinase class, and that the kinase domain is closely related to gluconate kinase and adenylate kinase. ATP is bound by the P-loop domain (residues 11-18). Formed by antiparallel dimerization of two PSTK monomers, the enzyme structure shows a deep groove with positive electrostatic potential. Located in this groove is the enzyme's active site, which biochemical and genetic data suggest is composed of Asp-41, Arg-44, Glu-55, Tyr-82, Tyr-83, Met-86, and Met-132. Based on structural comparison with Escherichia coli adenylate kinase a docking model was generated that assigns these amino acids to the recognition of the terminal A76-Ser moieties of Ser-tRNA(Sec). The geometry and electrostatic environment of the groove in MjPSTK are perfectly complementary to the unusually long acceptor helix of tRNA(Sec).
authors.affiliation: Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Yuhei
authors.initials: Y
authors.lastname: Araiso
authors.forename: R Lynn
authors.initials: RL
authors.lastname: Sherrer
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Ishitani
authors.forename: Joanne M L
authors.initials: JM
authors.lastname: Ho
authors.forename: Dieter
authors.initials: D
authors.lastname: Söll
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D003460:Crystallization; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D005816:Genetic Complementation Test; D017015:Methanococcales / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000378:metabolism*; D017279:Selenocysteine / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D012346:RNA, Transfer, Amino Acyl; C112705:selenocysteinyl-tRNA; D017279:Selenocysteine; D017346:Protein Serine-Threonine Kinases