1K2G | pdb_00001k2g

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

• PDB DOI: https://doi.org/10.2210/pdb1K2G/pdb
• NAKB: 1K2G

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-09-27 Released: 2002-05-08 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

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

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.

(2002) RNA 8: 440-451

• PubMed: 11991639 
• DOI: https://doi.org/10.1017/s1355838202026043
• Primary Citation Related Structures: 
  1K2G


• 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.

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Organizational Affiliation: 
• Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.11 kDa 
• Atom Count: 471 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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'	A	22	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-08 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2002-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection