3S5A

ABH2 cross-linked to undamaged dsDNA-2 with cofactors

3S5A の概要

• エントリーDOI: 10.2210/pdb3s5a/pdb
• 関連するPDBエントリー: 3BTY 3S57
• 分子名称: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, 5'-D(*CP*TP*GP*TP*CP*TP*CP*AP*CP*TP*GP*TP*CP*G)-3', 5'-D(*TP*CP*GP*AP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3', ... (8 entities in total)
• 機能のキーワード: protein-dna complex, double helix, jelly-roll fold, dioxygenase, dna binding, cross-linking, oxidoreductase-dna complex, oxidoreductase/dna
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Nucleus: Q6NS38
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 32357.66

構造登録者

Yi, C.,Chen, B.,Qi, B.,Ramirez, B.,Zhang, W.,Jia, G.,Zhang, L.,Li, C.Q.,Dinner, A.R.,Yang, C.-G.,He, C. (登録日: 2011-05-21, 公開日: 2012-06-06, 最終更新日: 2024-03-20)

主引用文献

Yi, C.,Chen, B.,Qi, B.,Zhang, W.,Jia, G.,Zhang, L.,Li, C.J.,Dinner, A.R.,Yang, C.G.,He, C.
Duplex interrogation by a direct DNA repair protein in search of base damage
Nat.Struct.Mol.Biol., 19:671-676, 2012

PubMed Abstract: ALKBH2 is a direct DNA repair dioxygenase guarding the mammalian genome against N(1)-methyladenine, N(3)-methylcytosine and 1,N(6)-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of human ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 has two previously unknown features: (i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability, and (ii) ALKBH2 does not have nor need a damage-checking site, which is critical for preventing spurious base cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.

PubMed: 22659876
DOI: 10.1038/nsmb.2320

実験手法

X-RAY DIFFRACTION (1.7 Å)