title: NMR studies of the effects of the 5'-phosphate group on conformational properties of 5-methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA(Arg)4.
abstract: 5-Methylaminomethyluridine (mnm5U) exists in the first position of the anticodon (position 34) of Escherichia coli tRNA4Arg for codons AGA/AGG. In the present study, the temperature dependence of the ribose-puckering equilibrium of pmnm5U was analyzed by proton NMR spectroscopy. Thus, the enthalpy difference (delta H) between the C2'-endo and C3'-endo forms was obtained at 0.65 kcal.mol-1. By comparison of the delta H values of pU and pmnm5U, the 5-substitution was found to increase the relative stability of the C3'-endo form over the C2'-endo form significantly (by 0.56 kcal.mol-1). Furthermore, this conformational "rigidity" was concluded to depend on the 5'-phosphate group, because nucleoside U exhibits only a negligible change in the ribose-puckering equilibrium upon the 5-methylaminomethyl substitution. Further NMR analyses and molecular dynamics calculations revealed that interactions between the 5-methylaminomethyl and 5'-phosphate groups of pmnm5U restrict the conformation about the glycosidic bond to a low anti form, enhancing steric repulsion between the 2-carbonyl and 2'-hydroxyl groups in the C2'-endo form. This intrinsic conformational rigidity of the mnm5U residue in position 34 may contribute to the correct codon recognition.
authors.affiliation: Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Sakamoto
authors.forename: G
authors.initials: G
authors.lastname: Kawai
authors.forename: S
authors.initials: S
authors.lastname: Watanabe
authors.forename: T
authors.initials: T
authors.lastname: Niimi
authors.forename: N
authors.initials: N
authors.lastname: Hayashi
authors.forename: Y
authors.initials: Y
authors.lastname: Muto
authors.forename: K
authors.initials: K
authors.lastname: Watanabe
authors.forename: T
authors.initials: T
authors.lastname: Satoh
authors.forename: M
authors.initials: M
authors.lastname: Sekine
authors.forename: S
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000926:Anticodon / Q000737:chemistry; D003196:Computer Graphics; D004926:Escherichia coli / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012347:RNA, Transfer, Arg / Q000737:chemistry*; D012266:Ribose; D013816:Thermodynamics; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000302:isolation & purification
chemical_list: C099620:5-methylaminomethyluridine; D000926:Anticodon; D012347:RNA, Transfer, Arg; D012266:Ribose; D014529:Uridine