7p9i | pdb_00007p9i

Structure of E.coli RlmJ in complex with an RNA conjugate (GAA-SAM)

spinqualitylabelsall models 7p9i, resolution 1.59Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7p9i is a 4 chain structure with sequence from Escherichia coli K-12 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.594Å Ligands: 6D6, GMP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RLMJ_ECOLI Specifically methylates the adenine in position 2030 of 23S rRNA. Nascent 23S rRNA seems to be the natural substrate. Appears to be not necessary for ribosome assembly. Seems to be required for the utilization of extracellular DNA as the sole source of carbon and energy. Publication Abstract from PubMed 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. Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase.,Meynier V, Iannazzo L, Catala M, Oerum S, Braud E, Atdjian C, Barraud P, Fonvielle M, Tisne C, Etheve-Quelquejeu M Nucleic Acids Res. 2022 May 17. pii: 6586874. doi: 10.1093/nar/gkac354. PMID:35580049 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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