6MAX
Crystal structure of Ribonuclease P protein from Thermotoga maritima in complex with purpurin
Summary for 6MAX
| Entry DOI | 10.2210/pdb6max/pdb |
| Related | 1NZ0 |
| Descriptor | Ribonuclease P protein component, SULFATE ION, Purpurin, ... (4 entities in total) |
| Functional Keywords | p protein, rna binding protein, hydrolase |
| Biological source | Thermotoga maritima |
| Total number of polymer chains | 1 |
| Total formula weight | 14272.77 |
| Authors | Torres-Larios, A.,Madrigal-Carrillo, E.A. (deposition date: 2018-08-28, release date: 2019-04-17, Last modification date: 2023-10-11) |
| Primary citation | Madrigal-Carrillo, E.A.,Diaz-Tufinio, C.A.,Santamaria-Suarez, H.A.,Arciniega, M.,Torres-Larios, A. A screening platform to monitor RNA processing and protein-RNA interactions in ribonuclease P uncovers a small molecule inhibitor. Nucleic Acids Res., 47:6425-6438, 2019 Cited by PubMed Abstract: Ribonucleoprotein (RNP) complexes and RNA-processing enzymes are attractive targets for antibiotic development owing to their central roles in microbial physiology. For many of these complexes, comprehensive strategies to identify inhibitors are either lacking or suffer from substantial technical limitations. Here, we describe an activity-binding-structure platform for bacterial ribonuclease P (RNase P), an essential RNP ribozyme involved in 5' tRNA processing. A novel, real-time fluorescence-based assay was used to monitor RNase P activity and rapidly identify inhibitors using a mini-helix and a pre-tRNA-like bipartite substrate. Using the mini-helix substrate, we screened a library comprising 2560 compounds. Initial hits were then validated using pre-tRNA and the pre-tRNA-like substrate, which ultimately verified four compounds as inhibitors. Biolayer interferometry-based binding assays and molecular dynamics simulations were then used to characterize the interactions between each validated inhibitor and the P protein, P RNA and pre-tRNA. X-ray crystallographic studies subsequently elucidated the structure of the P protein bound to the most promising hit, purpurin, and revealed how this inhibitor adversely affects tRNA 5' leader binding. This integrated platform affords improved structure-function studies of RNA processing enzymes and facilitates the discovery of novel regulators or inhibitors. PubMed: 30997498DOI: 10.1093/nar/gkz285 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.42 Å) |
Structure validation
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