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Solution structure of an RNA fragment with the P7/P9.0 region and the 3′-terminal guanosine of the Tetrahymena group I intron

Published online by Cambridge University Press:  24 April 2002

AYA KITAMURA ,
YUTAKA MUTO ,
SATORU WATANABE ,
INSIL KIM ,
TAKUHIRO ITO ,
YOICHI NISHIYA ,
KENSAKU SAKAMOTO ,
TAKASHI OHTSUKI ,
GOTA KAWAI  and
KIMITSUNA WATANABE
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AYA KITAMURA
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
YUTAKA MUTO
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
SATORU WATANABE
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan Present address: Biophysics Division, National Cancer Center Research Institute, Tsukiji, Chuou-ku, Tokyo, Japan.
INSIL KIM
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
TAKUHIRO ITO
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
YOICHI NISHIYA
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan Present address: Tokyo Research Laboratories, Kyowa Hakko Kogyo Co., Ltd., Asahi-machi, Machida-shi, Tokyo, Japan.
KENSAKU SAKAMOTO
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
TAKASHI OHTSUKI
Affiliation:
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
GOTA KAWAI
Affiliation:
Department of Industrial Chemistry, Chiba Institute of Technology, Narashino, Chiba, Japan
KIMITSUNA WATANABE
Affiliation:
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
KAZUMI HOSONO
Affiliation:
Department of Industrial Chemistry, Chiba Institute of Technology, Narashino, Chiba, Japan Present address: Nippon Sanso Co., Nishi-shin bashi, Minato-ku, Tokyo, Japan.
HIROSHI TAKAKU
Affiliation:
Department of Industrial Chemistry, Chiba Institute of Technology, Narashino, Chiba, Japan
ETSUKO KATOH
Affiliation:
Biochemistry Department, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki, Japan
TOSHIMASA YAMAZAKI
Affiliation:
Biochemistry Department, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki, Japan
TAN INOUE
Affiliation:
Graduate School of Biostudies, Kyoto University, Kyoto, Japan
SHIGEYUKI YOKOYAMA
Affiliation:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
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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[bull ]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[bull ]C311 and C262[bull ]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[bull ]G312 and G413[bull ]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.

Keywords

NMRribozymeRNA structureself-splicing
Type
Research Article
Information
RNA , Volume 8 , Issue 4 , April 2002 , pp. 440 - 451
Copyright
2002 RNA Society

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