Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.
In the second step of the two consecutive transesterifications of the self-splicing reaction of the group I intron, the conserved guanosine at the 3' terminus of the intron (omegaG) binds to the guanosine-binding site (GBS) in the intron. In the present study, we designed a 22-nt model RNA (GBS/omegaG) including the GBS and omegaG from the Tetrahymena group I intron, and determined the solution structure by NMR methods. In this structure, omegaG is recognized by the formation of a base triple with the G264 x C311 base pair, and this recognition is stabilized by the stacking interaction between omegaG and C262. The bulged structure at A263 causes a large helical twist angle (40 +/- 80) between the G264 x C311 and C262 x G312 base pairs. We named this type of binding pocket with a bulge and a large twist, formed on the major groove, a "Bulge-and-Twist" (BT) pocket. With another twist angle between the C262 x G312 and G413 x C313 base pairs (45 +/- 100), the axis of GBS/omegaG is kinked at the GBS region. This kinked axis superimposes well on that of the corresponding region in the structure model built on a 5.0 A resolution electron density map (Golden et al., Science, 1998, 282:345-358). This compact structure of the GBS is also consistent with previous biochemical studies on group I introns. The BT pockets are also found in the arginine-binding site of the HIV-TAR RNA, and within the 16S rRNA and the 23S rRNA.
Kitamura
Aya
A
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Japan.
Muto
Yutaka
Y
Watanabe
Satoru
S
Kim
Insil
I
Ito
Takuhiro
T
Nishiya
Yoichi
Y
Sakamoto
Kensaku
K
Ohtsuki
Takashi
T
Kawai
Gota
G
Watanabe
Kimitsuna
K
Hosono
Kazumi
K
Takaku
Hiroshi
H
Katoh
Etsuko
E
Yamazaki
Toshimasa
T
Inoue
Tan
T
Yokoyama
Shigeyuki
S
D000818:Animals; D006151:Guanosine / Q000737:chemistry*; D007438:Introns; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D016053:RNA, Protozoan / Q000737:chemistry*; D012996:Solutions; D013768:Tetrahymena / Q000235:genetics*
D016053:RNA, Protozoan; D012996:Solutions; D006151:Guanosine