7P9I
Structure of E.coli RlmJ in complex with an RNA conjugate (GAA-SAM)
Summary for 7P9I
| Entry DOI | 10.2210/pdb7p9i/pdb |
| Related | 6QDX 7P8Q 7P9O |
| Descriptor | Ribosomal RNA large subunit methyltransferase J, RNA conjugate (GAA-SAM), 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine, ... (4 entities in total) |
| Functional Keywords | rna mtases, methyltransferase, sam analogue, m6a, rna binding, sam conjugate, rlmj, conjugate analogue, rna recognition, bisubstrate analogue, rna binding protein |
| Biological source | Escherichia coli K-12 More |
| Total number of polymer chains | 4 |
| Total formula weight | 66585.48 |
| Authors | Meynier, V.,Catala, M.,Oerum, S.,Barraud, P.,Tisne, C. (deposition date: 2021-07-27, release date: 2022-06-01, Last modification date: 2024-01-31) |
| Primary citation | Meynier, V.,Iannazzo, L.,Catala, M.,Oerum, S.,Braud, E.,Atdjian, C.,Barraud, P.,Fonvielle, M.,Tisne, C.,Etheve-Quelquejeu, M. Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase. Nucleic Acids Res., 50:5793-5806, 2022 Cited by PubMed Abstract: Chemical synthesis of RNA conjugates has opened new strategies to study enzymatic mechanisms in RNA biology. To gain insights into poorly understood RNA nucleotide methylation processes, we developed a new method to synthesize RNA-conjugates for the study of RNA recognition and methyl-transfer mechanisms of SAM-dependent m6A RNA methyltransferases. These RNA conjugates contain a SAM cofactor analogue connected at the N6-atom of an adenosine within dinucleotides, a trinucleotide or a 13mer RNA. Our chemical route is chemo- and regio-selective and allows flexible modification of the RNA length and sequence. These compounds were used in crystallization assays with RlmJ, a bacterial m6A rRNA methyltransferase. Two crystal structures of RlmJ in complex with RNA-SAM conjugates were solved and revealed the RNA-specific recognition elements used by RlmJ to clamp the RNA substrate in its active site. From these structures, a model of a trinucleotide bound in the RlmJ active site could be built and validated by methyltransferase assays on RlmJ mutants. The methyl transfer by RlmJ could also be deduced. This study therefore shows that RNA-cofactor conjugates are potent molecular tools to explore the active site of RNA modification enzymes. PubMed: 35580049DOI: 10.1093/nar/gkac354 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.594 Å) |
Structure validation
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