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.
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.
Sakamoto
K
K
Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan.
Kawai
G
G
Watanabe
S
S
Niimi
T
T
Hayashi
N
N
Muto
Y
Y
Watanabe
K
K
Satoh
T
T
Sekine
M
M
Yokoyama
S
S
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
C099620:5-methylaminomethyluridine; D000926:Anticodon; D012347:RNA, Transfer, Arg; D012266:Ribose; D014529:Uridine