1K2G

Structural basis for the 3'-terminal guanosine recognition by the group I intron

Summary for 1K2G

• Entry DOI: 10.2210/pdb1k2g/pdb
• Descriptor: 5'-R(*CP*AP*GP*AP*CP*UP*UP*CP*GP*GP*UP*CP*GP*CP*AP*GP*AP*GP*AP*UP*GP*G)-3' (1 entity in total)
• Functional Keywords: base triple recognition of a guanosine, uucg tetraloop, gaga tetraloop, rna
• Total number of polymer chains: 1
• Total formula weight: 7113.29

Authors

Kitamura, Y.,Muto, Y.,Watanabe, S.,Kim, I.,Ito, T.,Nishiya, Y.,Sakamoto, K.,Ohtsuki, T.,Kawai, G.,Watanabe, K.,Hosono, K.,Takaku, H.,Katoh, E.,Yamazaki, T.,Inoue, T.,Yokoyama, S. (deposition date: 2001-09-27, release date: 2002-05-08, Last modification date: 2024-05-22)

Primary citation

Kitamura, A.,Muto, Y.,Watanabe, S.,Kim, I.,Ito, T.,Nishiya, Y.,Sakamoto, K.,Ohtsuki, T.,Kawai, G.,Watanabe, K.,Hosono, K.,Takaku, H.,Katoh, E.,Yamazaki, T.,Inoue, T.,Yokoyama, S.
Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.
RNA, 8:440-451, 2002

PubMed 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 (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.

PubMed: 11991639
DOI: 10.1017/S1355838202026043

Experimental method

SOLUTION NMR