title: Major identity determinants in the "augmented D helix" of tRNA(Glu) from Escherichia coli.
abstract: By a kinetic analysis of 59 variant transcripts of Escherichia coli tRNA(Glu) with glutamyl-tRNA synthetase (GluRS), the U11.A24 base-pair, the U13.G22..A46 base-triple, and the lack of residue 47 (delta47) were found to serve as major determinants for tRNA(Glu) identity. This is the first system for which major identity determinants are reported to be clustered in the "augmented D helix", consisting of the D stem with some neighboring residues and the variable loop. Other identity determinants are U34, U35, C36 and A37 in the anticodon loop, and G1.C72 and U2.A71 in the acceptor stem. Phosphate-group protection by GluRS from ethylnitrosourea was observed most strongly for the minor groove side of D-stem helix, indicating that GluRs tightly binds to the D stem for recognition, on the minor groove side, of the potent identity-determinant groups of the U11.A24 and U13.G22 base-pairs. A46 is not involved in direct recognition by GluRS; the U13.G22..A46 base-triple is required probably for formation of the structural features that are recognized by GluRS. In this context, the essential role of characteristic delta47 in tRNA(Glu) identity may be to maintain the U13.G22..A46 base-triple.
authors.affiliation: Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Sekine
authors.forename: O
authors.initials: O
authors.lastname: Nureki
authors.forename: K
authors.initials: K
authors.lastname: Sakamoto
authors.forename: T
authors.initials: T
authors.lastname: Niimi
authors.forename: M
authors.initials: M
authors.lastname: Tateno
authors.forename: M
authors.initials: M
authors.lastname: Go
authors.forename: T
authors.initials: T
authors.lastname: Kohno
authors.forename: A
authors.initials: A
authors.lastname: Brisson
authors.forename: J
authors.initials: J
authors.lastname: Lapointe
authors.forename: S
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000926:Anticodon / Q000235:genetics; D001482:Base Composition; D001483:Base Sequence; D003001:Cloning, Molecular; D003062:Codon / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000737:chemistry*; D005038:Ethylnitrosourea / Q000378:metabolism; D005975:Glutamate-tRNA Ligase / Q000378:metabolism; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry; D011485:Protein Binding; D012351:RNA, Transfer, Gln / Q000737:chemistry / Q000378:metabolism; D012352:RNA, Transfer, Glu / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D000926:Anticodon; D003062:Codon; D009843:Oligoribonucleotides; D012351:RNA, Transfer, Gln; D012352:RNA, Transfer, Glu; D016601:RNA-Binding Proteins; D005975:Glutamate-tRNA Ligase; D005038:Ethylnitrosourea