4NRP

Crystal structure of human ALKBH5 in complex with N-oxalylglycine

4NRP の概要

• エントリーDOI: 10.2210/pdb4nrp/pdb
• 関連するPDBエントリー: 4NRM 4NRO
• 分子名称: RNA demethylase ALKBH5, MANGANESE (II) ION, N-OXALYLGLYCINE, ... (4 entities in total)
• 機能のキーワード: alkbh5, 6-methyl adenosine, protein/dna interaction, human dioxygenase, metal-binding, nucleus, demethylation, rna repair, oxidoreductase
• 由来する生物種: Homo sapiens
• 細胞内の位置: Nucleus speckle : Q6P6C2
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 26587.15

構造登録者

Feng, C.,Chen, Z.,Liu, Y. (登録日: 2013-11-27, 公開日: 2014-03-19, 最終更新日: 2024-10-16)

主引用文献

Feng, C.,Liu, Y.,Wang, G.,Deng, Z.,Zhang, Q.,Wu, W.,Tong, Y.,Cheng, C.,Chen, Z.
Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition
J.Biol.Chem., 289:11571-11583, 2014

PubMed Abstract: N(6)-Methylation of adenosine is the most ubiquitous and abundant modification of nucleoside in eukaryotic mRNA and long non-coding RNA. This modification plays an essential role in the regulation of mRNA translation and RNA metabolism. Recently, human AlkB homolog 5 (Alkbh5) and fat mass- and obesity-associated protein (FTO) were shown to erase this methyl modification on mRNA. Here, we report five high resolution crystal structures of the catalytic core of Alkbh5 in complex with different ligands. Compared with other AlkB proteins, Alkbh5 displays several unique structural features on top of the conserved double-stranded β-helix fold typical of this protein family. Among the unique features, a distinct "lid" region of Alkbh5 plays a vital role in substrate recognition and catalysis. An unexpected disulfide bond between Cys-230 and Cys-267 is crucial for the selective binding of Alkbh5 to single-stranded RNA/DNA by bringing a "flipping" motif toward the central β-helix fold. We generated a substrate binding model of Alkbh5 based on a demethylation activity assay of several structure-guided site-directed mutants. Crystallographic and biochemical studies using various analogs of α-ketoglutarate revealed that the active site cavity of Alkbh5 is much smaller than that of FTO and preferentially binds small molecule inhibitors. Taken together, our findings provide a structural basis for understanding the substrate recognition specificity of Alkbh5 and offer a foundation for selective drug design against AlkB members.

PubMed: 24616105
DOI: 10.1074/jbc.M113.546168

実験手法

X-RAY DIFFRACTION (1.8 Å)