5DUN
The crystal structure of OMe substituted twister ribozyme
Summary for 5DUN
| Entry DOI | 10.2210/pdb5dun/pdb |
| Descriptor | RNA (54-MER), MAGNESIUM ION, POTASSIUM ION, ... (4 entities in total) |
| Functional Keywords | ome, twister, rna, ribozyme |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 17639.93 |
| Authors | Ren, A.,Patel, D.J.,Micura, R.,Rajashankar, K.R. (deposition date: 2015-09-19, release date: 2015-10-28, Last modification date: 2023-09-27) |
| Primary citation | Kosutic, M.,Neuner, S.,Ren, A.,Flur, S.,Wunderlich, C.,Mairhofer, E.,Vusurovic, N.,Seikowski, J.,Breuker, K.,Hobartner, C.,Patel, D.J.,Kreutz, C.,Micura, R. A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class. Angew.Chem.Int.Ed.Engl., 54:15128-15133, 2015 Cited by PubMed Abstract: Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pKa value of 5.1 was determined for a (13) C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg(2+) ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn(2+) or Cd(2+) accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X-ray structure of a 2'-OCH3 -U5 modified twister ribozyme. PubMed: 26473980DOI: 10.1002/anie.201506601 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.64 Å) |
Structure validation
Download full validation report
