1OW9
NMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site
Summary for 1OW9
| Entry DOI | 10.2210/pdb1ow9/pdb |
| Related | 1E4P 1HWQ |
| NMR Information | BMRB: 5852 |
| Descriptor | A mimic of the VS Ribozyme Hairpin Substrate (1 entity in total) |
| Functional Keywords | vs ribozyme, substrate hairpin, cleavage site, sheared g-a base pairs, shared sheared g-a base pairs, magnesium ion binding, gnra tetraloop, riboze zipper, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 7488.58 |
| Authors | Hoffmann, B.,Mitchell, G.T.,Gendron, P.,Major, F.,Andersen, A.A.,Collins, R.A.,Legault, P. (deposition date: 2003-03-28, release date: 2003-05-20, Last modification date: 2024-05-22) |
| Primary citation | Hoffmann, B.,Mitchell, G.T.,Gendron, P.,Major, F.,Andersen, A.A.,Collins, R.A.,Legault, P. NMR Structure of the Active Conformation of the Varkud satellite Ribozyme Cleavage Site Proc.Natl.Acad.Sci.USA, 100:7003-7008, 2003 Cited by PubMed Abstract: Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme involves a structural change in the stem-loop I substrate from an inactive to an active conformation. We have determined the NMR solution structure of a mutant stem-loop I that mimics the active conformation of the cleavage site internal loop. This structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. The active internal loop displays different base-pairing interactions and forms a novel RNA fold composed exclusively of sheared G-A base pairs. From chemical-shift mapping we identified two Mg2+ binding sites in the active internal loop. One of the Mg2+ binding sites forms in the active but not the inactive conformation of the internal loop and is likely important for catalysis. Using the structure comparison program mc-search, we identified the active internal loop fold in other RNA structures. In Thermus thermophilus 16S rRNA, this RNA fold is directly involved in a long-range tertiary interaction. An analogous tertiary interaction may form between the active internal loop of the substrate and the catalytic domain of the VS ribozyme. The combination of NMR and bioinformatic approaches presented here has identified a novel RNA fold and provides insights into the structural basis of catalytic function in the Neurospora VS ribozyme. PubMed: 12782785DOI: 10.1073/pnas.0832440100 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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