7P8Q

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

7P8Q の概要

• エントリーDOI: 10.2210/pdb7p8q/pdb
• 関連するPDBエントリー: 6QDX
• 分子名称: Ribosomal RNA large subunit methyltransferase J, RNA conjugate (GA-SAM), 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine, ... (4 entities in total)
• 機能のキーワード: rna mtases, methyltransferase, sam analogue, m6a, rna binding, sam conjugate, rlmj, conjugate analogue, rna recognition, bisubstrate analogue, rna binding protein
• 由来する生物種: Escherichia coli K-12; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 32963.54

構造登録者

Meynier, V.,Catala, M.,Oerum, S.,Barraud, P.,Tisne, C. (登録日: 2021-07-23, 公開日: 2022-06-01, 最終更新日: 2024-01-31)

主引用文献

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

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: 35580049
DOI: 10.1093/nar/gkac354

実験手法

X-RAY DIFFRACTION (2.289 Å)