2h49

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The NMR Structure of an Internal Loop from 23S Ribosomal RNA of Deinococcus radiodurans Differs from the Structure in the Crystal of the Ribosomal Subunit

Overview

Internal loops play an important role in structure and folding of RNA and, in recognition of RNA by other molecules such as proteins and ligands. An, understanding of internal loops with propensities to form a particular, structure will help predict RNA structure, recognition, and function. The, structures of internal loops 5' 1009CUAAG1013 3'/3' 1168GAAGC1164 5' and, 5' 998CUAAG1002 3'/3' 1157GAAGC1153 5' from helix 40 of the large subunit, rRNA in Deinococcus radiodurans and Escherichia coli, respectively, are, phylogenetically conserved, suggesting functional relevance. The, energetics and NMR solution structure of the loop were determined in the, duplex 5' 1GGCUAAGAC9 3'/3' 18CCGAAGCUG10 5'. The internal loop forms a, different structure in solution and in the crystal structures of the, ribosomal subunits. In particular, the crystal structures have a bulged, out adenine at the equivalent of position A15 and a reverse Hoogsteen UA, pair (trans Watson-Crick/Hoogsteen UA) at the equivalent of U4 and A14, whereas the solution structure has a single hydrogen bond UA pair (cis, Watson-Crick/sugar edge A15U4) between U4 and A15 and a sheared AA pair, (trans Hoogsteen/sugar edge A14A5) between A5 and A14. There is, cross-strand stacking between A6 and A14 (A6/A14/A15 stacking pattern) in, the NMR structure. All three structures have a sheared GA pair (trans, Hoogsteen/sugar edge A6G13) at the equivalent of A6 and G13. The internal, loop has contacts with ribosomal protein L20 and other parts of the RNA in, the crystal structures. These contacts presumably provide the free energy, to rearrange the base pairing in the loop. Evidently, molecular, recognition of this internal loop involves induced fit binding, which, could confer several advantages. The predicted thermodynamic stability of, the loop agrees with the experimental value, even though the thermodynamic, model assumes a Watson-Crick UA pair.

About this Structure

2H49 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits., Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH, Biochemistry. 2006 Oct 3;45(39):11776-89. PMID:17002278

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