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4NRP

Crystal structure of human ALKBH5 in complex with N-oxalylglycine

4NRP の概要
エントリーDOI10.2210/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
Cited by
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
主引用文献が同じPDBエントリー
実験手法
X-RAY DIFFRACTION (1.8 Å)
構造検証レポート
Validation report summary of 4nrp
検証レポート(詳細版)ダウンロードをダウンロード

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件を2025-07-23に公開中

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