4Z3A

Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU mismatch

4Z3A の概要

• エントリーDOI: 10.2210/pdb4z3a/pdb
• 関連するPDBエントリー: 4XEG 4Z47 4Z7B 4Z7Z 5CYS
• 分子名称: G/T mismatch-specific thymine DNA glycosylase, DNA (28-MER), ... (4 entities in total)
• 機能のキーワード: protein-dna complex, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 40190.67

構造登録者

Pozharski, E.,Malik, S.S.,Drohat, A.C. (登録日: 2015-03-31, 公開日: 2015-09-16, 最終更新日: 2023-09-27)

主引用文献

Malik, S.S.,Coey, C.T.,Varney, K.M.,Pozharski, E.,Drohat, A.C.
Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.
Nucleic Acids Res., 43:9541-9552, 2015

PubMed Abstract: Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G ·: T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten-eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 Å) structures of TDG enzyme-product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water-mediated enzyme-substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme-product complex.

PubMed: 26358812
DOI: 10.1093/nar/gkv890

実験手法

X-RAY DIFFRACTION (1.72 Å)