1TBK
NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.
Summary for 1TBK
| Entry DOI | 10.2210/pdb1tbk/pdb |
| Descriptor | VS ribozyme stem-loop V (1 entity in total) |
| Functional Keywords | u-turn; hairpin, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 5419.26 |
| Authors | Campbell, D.O.,Legault, P. (deposition date: 2004-05-20, release date: 2005-03-01, Last modification date: 2024-05-22) |
| Primary citation | Campbell, D.O.,Legault, P. Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem-Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping Biochemistry, 44:4157-4170, 2005 Cited by PubMed Abstract: An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme. PubMed: 15766243DOI: 10.1021/bi047963l PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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