1MUV

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

Summary for 1MUV

• Entry DOI: 10.2210/pdb1muv/pdb
• Related: 1GID 1MV1 1MV2 1MV6 1YFV
• NMR Information: BMRB: 5614
• Descriptor: 5'-R(*GP*GP*CP*AP*AP*GP*CP*CP*U)-3' (1 entity in total)
• Functional Keywords: ribonucleic acid, duplex, tandem mismatch, aa mismatch, rna
• Total number of polymer chains: 2
• Total formula weight: 5741.57

Authors

Znosko, B.M.,Burkard, M.E.,Schroeder, S.J.,Krugh, T.R.,Turner, D.H. (deposition date: 2002-09-24, release date: 2002-12-18, Last modification date: 2024-05-22)

Primary citation

Znosko, B.M.,Burkard, M.E.,Schroeder, S.J.,Krugh, T.R.,Turner, D.H.
Sheared Aanti-Aanti Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2
Biochemistry, 41:14969-14977, 2002

PubMed Abstract: 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.

PubMed: 12475246
DOI: 10.1021/bi020326f

Experimental method

SOLUTION NMR