2RPT
Structure of the CC mismatch from the thymidylate synthase binding site 1 hairpin and analysis of its interaction with paromomycin
Summary for 2RPT
| Entry DOI | 10.2210/pdb2rpt/pdb |
| Descriptor | RNA (5'-R(*GP*GP*CP*CP*CP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*CP*GP*GP*CP*C)-3') (1 entity in total) |
| Functional Keywords | nmr spectroscopy, rna structure, paromomycin, aminoglycoside-rna interaction, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 6450.94 |
| Authors | Tavares, T.J.,Johnson, P.E. (deposition date: 2008-08-23, release date: 2009-08-25, Last modification date: 2024-05-29) |
| Primary citation | Tavares, T.J.,Beribisky, A.V.,Johnson, P.E. Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin Rna, 15:911-922, 2009 Cited by PubMed Abstract: The structure of a cytosine-cytosine (CC) mismatch-containing RNA molecule derived from a hairpin structure in the thymidylate synthase mRNA that binds the aminoglycoside paromomycin with high affinity was determined using nuclear magnetic resonance (NMR) spectroscopy. The cytosines in the mismatch form a noncanonical base pair where both cytosines are uncharged and stack within the stem of the RNA structure. Binding to paromomycin was analyzed using isothermal titration calorimetry (ITC) to demonstrate the necessity of the CC mismatch and to determine the affinity dissociation constant of this RNA to paromomycin to be 0.5 +/- 0.3 microM. The CC mismatch, and the neighboring GC base pairs experienced the highest degree of chemical shift changes in their H6 and H5 resonances indicating that paromomycin binds in the major groove at the CC mismatch site. In comparing the structure of CC mismatch RNA with a fully Watson-Crick GC base paired stem, the CC mismatch is shown to confer a widening of the major groove. This widening, combined with the dynamic nature of the CC mismatch, enables binding of paromomycin to this RNA molecule. PubMed: 19329536DOI: 10.1261/rna.1514909 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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