Abstract
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 (ωG) binds to the guanosine-binding site (GBS) in the intron. In the present study, we designed a 22-nt model RNA (GBS/ωG) including the GBS and ωG from the Tetrahymena group I intron, and determined the solution structure by NMR methods. In this structure, ωG is recognized by the formation of a base triple with the G264·C311 base pair, and this recognition is stabilized by the stacking interaction between ωG and C262. The bulged structure at A263 causes a large helical twist angle (40 ± 8°) between the G264·C311 and C262·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·G312 and G413·C313 base pairs (45 ± 10°), the axis of GBS/ωG 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 Å 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.
| Original language | English |
|---|---|
| Pages (from-to) | 440-451 |
| Number of pages | 12 |
| Journal | RNA |
| Volume | 8 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - 2002 |
| Externally published | Yes |
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Keywords
- NMR
- Ribozyme
- RNA structure
- Self-splicing
ASJC Scopus subject areas
- Genetics
- Molecular Biology
Cite this
Solution structure of an RNA fragment with the P7/P9.0 region and the 3′-terminal guanosine of the Tetrahymena group I intron. / Kitamura, Aya; Muto, Yutaka; Watanabe, Satoru; Kim, Insil; Ito, Takuhiro; Nishiya, Yoichi; Sakamoto, Kensaku; Ohtsuki, Takashi; Kawai, Gota; Watanabe, Kimitsuna; Hosono, Kazumi; Takaku, Hiroshi; Katoh, Etsuko; Yamazaki, Toshimasa; Inoue, Tan; Yokoyama, Shigeyuki.
In: RNA, Vol. 8, No. 4, 2002, p. 440-451.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Solution structure of an RNA fragment with the P7/P9.0 region and the 3′-terminal guanosine of the Tetrahymena group I intron
AU - Kitamura, Aya
AU - Muto, Yutaka
AU - Watanabe, Satoru
AU - Kim, Insil
AU - Ito, Takuhiro
AU - Nishiya, Yoichi
AU - Sakamoto, Kensaku
AU - Ohtsuki, Takashi
AU - Kawai, Gota
AU - Watanabe, Kimitsuna
AU - Hosono, Kazumi
AU - Takaku, Hiroshi
AU - Katoh, Etsuko
AU - Yamazaki, Toshimasa
AU - Inoue, Tan
AU - Yokoyama, Shigeyuki
PY - 2002
Y1 - 2002
N2 - 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 (ωG) binds to the guanosine-binding site (GBS) in the intron. In the present study, we designed a 22-nt model RNA (GBS/ωG) including the GBS and ωG from the Tetrahymena group I intron, and determined the solution structure by NMR methods. In this structure, ωG is recognized by the formation of a base triple with the G264·C311 base pair, and this recognition is stabilized by the stacking interaction between ωG and C262. The bulged structure at A263 causes a large helical twist angle (40 ± 8°) between the G264·C311 and C262·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·G312 and G413·C313 base pairs (45 ± 10°), the axis of GBS/ωG 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 Å 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.
AB - 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 (ωG) binds to the guanosine-binding site (GBS) in the intron. In the present study, we designed a 22-nt model RNA (GBS/ωG) including the GBS and ωG from the Tetrahymena group I intron, and determined the solution structure by NMR methods. In this structure, ωG is recognized by the formation of a base triple with the G264·C311 base pair, and this recognition is stabilized by the stacking interaction between ωG and C262. The bulged structure at A263 causes a large helical twist angle (40 ± 8°) between the G264·C311 and C262·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·G312 and G413·C313 base pairs (45 ± 10°), the axis of GBS/ωG 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 Å 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.
KW - NMR
KW - Ribozyme
KW - RNA structure
KW - Self-splicing
UR - http://www.scopus.com/inward/record.url?scp=0036235683&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0036235683&partnerID=8YFLogxK
U2 - 10.1017/S1355838202026043
DO - 10.1017/S1355838202026043
M3 - Article
C2 - 11991639
AN - SCOPUS:0036235683
VL - 8
SP - 440
EP - 451
JO - RNA
JF - RNA
SN - 1355-8382
IS - 4
ER -