1muv

From Proteopedia

Sheared A(anti)-A(anti) Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2

Overview

The 5'(rGGCAAGCCU)(2) duplex contains tandem A.A pairs. The, three-dimensional structure of the 5'(rGGCAAGCCU)(2) duplex was modeled by, molecular dynamics and energy minimization with NMR-derived distance and, dihedral angle restraints. Although the 5'(rCAAG)(2) loop is, thermodynamically destabilizing by 1.1 kcal/mol, the tandem A.A pairs, adopt a predominant conformation: a sheared anti-anti (A.A trans, Hoogsteen/Sugar-edge) alignment similar to that observed in the crystal, structure of the P4-P6 domain of the Tetrahymena thermophila intron [Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C., E., Cech, T. R., and Doudna, J. A. (1996) Science 273, 1678-1685]. The, NMR-derived structure of the 5'(rGGCAAGCCU)(2) duplex exhibits, cross-strand hydrogen bonds from N3 of A4 to an amino hydrogen of A5 and, from the 2' oxygen of the A4 sugar to the other amino hydrogen of A5. An, intrastrand hydrogen bond is formed from the 2' OH hydrogen of A4 to O5', of A5. The cross-strand A5 bases are stacked. The Watson-Crick G-C regions, are essentially A-form. The sheared anti-anti (A.A trans, Hoogsteen/Sugar-edge) alignment provides potential contact sites for, tertiary interactions and, therefore, is a possible target site for, therapeutics. Thus, thermodynamically destabilizing internal loops can be, preorganized for tertiary interactions or ligand binding.

About this Structure

1MUV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2., Znosko BM, Burkard ME, Schroeder SJ, Krugh TR, Turner DH, Biochemistry. 2002 Dec 17;41(50):14969-77. PMID:12475246

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