6XJZ
Crystal structure of a self-alkylating ribozyme - apo form
Summary for 6XJZ
| Entry DOI | 10.2210/pdb6xjz/pdb |
| Descriptor | Self-alkylating ribozyme (58-MER), Fab HAVx Heavy Chain, Fab HAVx Light Chain, ... (4 entities in total) |
| Functional Keywords | self-alkylating ribozyme, antibody-assisted rna crystallography, rna catalysis, rna-immune system complex, rna/immune system |
| Biological source | Homo sapiens (Human) More |
| Total number of polymer chains | 6 |
| Total formula weight | 145227.39 |
| Authors | Koirala, D.,Piccirilli, J.A. (deposition date: 2020-06-24, release date: 2022-01-19, Last modification date: 2023-10-18) |
| Primary citation | Krochmal, D.,Shao, Y.,Li, N.S.,DasGupta, S.,Shelke, S.A.,Koirala, D.,Piccirilli, J.A. Structural basis for substrate binding and catalysis by a self-alkylating ribozyme. Nat.Chem.Biol., 18:376-384, 2022 Cited by PubMed Abstract: Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable the development of better tools for studying RNA. Nevertheless, high-resolution structures and underlying catalytic mechanisms for members of this ribozyme class remain elusive. Here, we focus on a self-alkylating ribozyme that catalyzes nitrogen-carbon bond formation between a specific guanine and a 2,3-disubstituted epoxide substrate and report the crystal structures of a self-alkylating ribozyme, including both alkylated and apo forms, at 1.71-Å and 2.49-Å resolution, respectively. The ribozyme assumes an elongated hairpin-like architecture preorganized to accommodate the epoxide substrate in a hook-shaped conformation. Observed reactivity of substrate analogs together with an inverse, log-linear pH dependence of the reaction rate suggests a requirement for epoxide protonation, possibly assisted by the ether oxygens within the substrate. PubMed: 35058645DOI: 10.1038/s41589-021-00950-z PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.488 Å) |
Structure validation
Download full validation report
