7MLW
Burkholderia sp. TJI49 Guanidine-I riboswitch
Summary for 7MLW
| Entry DOI | 10.2210/pdb7mlw/pdb |
| Descriptor | Guanidine-I riboswitch, GUANIDINE, PHOSPHATE ION, ... (7 entities in total) |
| Functional Keywords | riboswitch, guanidine, potassium, ion, a-minor, rna |
| Biological source | Burkholderia sp. TJI49 |
| Total number of polymer chains | 1 |
| Total formula weight | 42270.05 |
| Authors | Trachman, R.J.,Ferre-D'Amare, A.R. (deposition date: 2021-04-29, release date: 2022-01-12, Last modification date: 2023-10-18) |
| Primary citation | Trachman 3rd, R.J.,Ferre-D'Amare, A.R. An uncommon [K + (Mg 2+ ) 2 ] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch. Rna, 27:1257-1264, 2021 Cited by PubMed Abstract: The widespread -I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the -I subtype-1 (Guanidine-I) riboswitch aptamer domain. Differing from the previously reported structures of orthologs from and , our structure reveals a chelated K ion adjacent to two Mg ions in the guanidine-binding pocket. Thermal melting analysis shows that K chelation, which induces localized conformational changes in the binding pocket, improves guanidinium-RNA interactions. Analysis of ribosome structures suggests that the [K(Mg)] ion triad is uncommon. It is, however, reminiscent of metal ion clusters found in the active sites of ribozymes and DNA polymerases. Previous structural characterization of -I subtype-2 RNAs, which bind the effector ligands ppGpp and PRPP, indicate that in those paralogs, an adenine responsible for K chelation in the Guanidine-I riboswitch is replaced by a pyrimidine. This mutation results in a water molecule and Mg ion binding in place of the K ion. Thus, our structural analysis demonstrates how ion and solvent chelation tune divergent ligand specificity and affinity among -I riboswitches. PubMed: 34257148DOI: 10.1261/rna.078824.121 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.7 Å) |
Structure validation
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