5ZMD

Crystal structure of FTO in complex with m6dA modified ssDNA

5ZMD の概要

• エントリーDOI: 10.2210/pdb5zmd/pdb
• 分子名称: Alpha-ketoglutarate-dependent dioxygenase FTO, DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3'), MANGANESE (II) ION, ... (5 entities in total)
• 機能のキーワード: rna demetheylase fto, m6a, substrate preference, rna binding protein, oxidoreductase-dna complex, oxidoreductase/dna
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 224936.28

構造登録者

Zhang, X.,Wei, L.H.,Luo, J.,Xiao, Y.,Liu, J.,Zhang, W.,Zhang, L.,Jia, G.F. (登録日: 2018-04-02, 公開日: 2019-04-10, 最終更新日: 2024-10-30)

主引用文献

Zhang, X.,Wei, L.H.,Wang, Y.,Xiao, Y.,Liu, J.,Zhang, W.,Yan, N.,Amu, G.,Tang, X.,Zhang, L.,Jia, G.
Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates.
Proc. Natl. Acad. Sci. U.S.A., 116:2919-2924, 2019

PubMed Abstract: FTO demethylates internal -methyladenosine (mA) and ,2'--dimethyladenosine (mA; at the cap +1 position) in mRNA, mA and mA in snRNA, and -methyladenosine (mA) in tRNA in vivo, and in vitro evidence supports that it can also demethylate -methyldeoxyadenosine (6mA), 3-methylthymine (3mT), and 3-methyluracil (mU). However, it remains unclear how FTO variously recognizes and catalyzes these diverse substrates. Here we demonstrate-in vitro and in vivo-that FTO has extensive demethylation enzymatic activity on both internal mA and cap mA Considering that 6mA, mA, and mA all share the same nucleobase, we present a crystal structure of human FTO bound to 6mA-modified ssDNA, revealing the molecular basis of the catalytic demethylation of FTO toward multiple RNA substrates. We discovered that () -methyladenine is the most favorable nucleobase substrate of FTO, () FTO displays the same demethylation activity toward internal mA and mA in the same RNA sequence, suggesting that the substrate specificity of FTO primarily results from the interaction of residues in the catalytic pocket with the nucleobase (rather than the ribose ring), and () the sequence and the tertiary structure of RNA can affect the catalytic activity of FTO. Our findings provide a structural basis for understanding the catalytic mechanism through which FTO demethylates its multiple substrates and pave the way forward for the structure-guided design of selective chemicals for functional studies and potential therapeutic applications.

PubMed: 30718435
DOI: 10.1073/pnas.1820574116

実験手法

X-RAY DIFFRACTION (3.3 Å)