9FN3
Crystal structure of the alkyltransferase ribozyme SAMURI co-crystalized with ProSeDMA
This is a non-PDB format compatible entry.
Summary for 9FN3
| Entry DOI | 10.2210/pdb9fn3/pdb |
| Related | 9FN2 |
| Descriptor | SAMURI-ProSeDMA, Se-2,6-diaminopurinribosyl-selenohomocysteineamide, MAGNESIUM ION, ... (4 entities in total) |
| Functional Keywords | ribozyme, sam-analogue, alkyltransferase, rna |
| Biological source | synthetic construct |
| Total number of polymer chains | 2 |
| Total formula weight | 38680.57 |
| Authors | Chen, H.A.,Okuda, T.,Lenz, A.K.,Scheitl, C.P.M.,Schindelin, H.,Hoebartner, C. (deposition date: 2024-06-07, release date: 2025-02-05, Last modification date: 2025-02-12) |
| Primary citation | Chen, H.A.,Okuda, T.,Lenz, A.K.,Scheitl, C.P.M.,Schindelin, H.,Hobartner, C. Structure and catalytic activity of the SAM-utilizing ribozyme SAMURI. Nat.Chem.Biol., 2025 Cited by PubMed Abstract: Ribozymes that catalyze site-specific RNA modification have recently gained increasing interest for their ability to mimic methyltransferase enzymes and for their application to install molecular tags. Recently, we reported SAMURI as a site-specific alkyltransferase ribozyme using S-adenosylmethionine (SAM) or a stabilized analog to transfer a methyl or propargyl group to N of an adenosine. Here, we report the crystal structures of SAMURI in the postcatalytic state. The structures reveal a three-helix junction with the catalytic core folded into four stacked layers, harboring the cofactor and the modified nucleotide. Detailed structure-activity analyses explain the cofactor scope and the structural basis for site selectivity. A structural comparison of SAMURI with SAM riboswitches sheds light on how the synthetic ribozyme overcomes the strategies of natural riboswitches to avoid self-methylation. Our results suggest that SAM and its analogs may serve as substrates for various RNA-catalyzed reactions, for which the corresponding ribozymes remain to be identified. PubMed: 39779902DOI: 10.1038/s41589-024-01808-w PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
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