8XWC

Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the substrate 8-oxoguanine DNA at pH 8.0 under 277 K

8XWC の概要

• エントリーDOI: 10.2210/pdb8xwc/pdb
• 分子名称: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'), DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'), N-glycosylase/DNA lyase, ... (8 entities in total)
• 機能のキーワード: dna, repair, lyase, dna-hydrolase complex, dna/hydrolase
• 由来する生物種: Homo sapiens; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 47640.50

構造登録者

Unno, M.,Koga, M.,Minowa, N.,Komuro, S.,Tanaka, Y. (登録日: 2024-01-16, 公開日: 2025-07-23, 最終更新日: 2025-08-13)

主引用文献

Unno, M.,Morikawa, M.,Sychrovsky, V.,Koga, M.,Minowa, N.,Komuro, S.,Shimizu, M.,Fukuta, M.,Tsuyuguchi, F.,Mano, H.,Ochi, Y.,Nakashima, K.,Okamoto, Y.,Saio, T.,Hattori, Y.,Tanaka, Y.
Capturing a glycosylase reaction intermediate in DNA repair by freeze-trapping of a pH-responsive hOGG1 mutant.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: The human 8-oxoguanine DNA glycosylase 1 (hOGG1) is a bifunctional DNA repair enzyme that possesses both glycosylase and AP-lyase activity. Its AP-lyase reaction mechanism had been revealed by crystallographic capturing of the intermediate adduct. However, no intermediate within the glycosylase reaction was reported to date and the relevant reaction mechanism thus remained unresolved. In this work, we studied the glycosylase reaction of hOGG1 by time-resolved crystallography and spectroscopic/enzymological analyses. To trigger the glycosylase reaction within a crystal, we created a pH-responsive mutant of hOGG1 in which lysine 249 (K249) has been replaced by histidine (H), and designated hOGG1(K249H). Using hOGG1(K249H), a reactive intermediate state of the hOGG1(K249H)-DNA complex was captured in crystal upon pH activation. An unprecedented, ribose-ring-opened hemiaminal structure at the 8-oxoguanine (oxoG) site was found. Based on the structure of the reaction intermediate and QM/MM (quantum mechanics/molecular mechanics) calculations, a glycosylase reaction pathway of hOGG1(K249H) was identified where the aspartic acid 268 (D268) acts as a proton donor to O4' of oxoG. Moreover, enzymologically derived pKa (4.5) of a catalytic residue indicated that the observed pKa can be attributed to the carboxy group of D268. Thus, a reaction mechanism of the glycosylase reaction by hOGG1(K249H) has been proposed.

PubMed: 40754315
DOI: 10.1093/nar/gkaf718

実験手法

X-RAY DIFFRACTION (1.45 Å)