Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12, Mansfield Road, Oxford OX1 5JJ, U.K.
Inorg Chem. 2024 Jun 10;63(23):10737-10755. doi: 10.1021/acs.inorgchem.4c01365. Epub 2024 May 23.
Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.
非血红素 Fe(II)和 2-氧代戊二酸（2OG）依赖性组蛋白赖氨酸去甲基酶 2A（KDM2A）催化组蛋白 H3 肽（H3K36me1/me2）中赖氨酸 36 位单甲基或二甲基的去甲基化，这在表观遗传调控中起着至关重要的作用，并可能涉及许多癌症。尽管已经研究了 KDMs 的总体催化机制，但 KDM2 与其他 KDMs 的催化方式仍不清楚。了解这些差异对于酶的重新设计至关重要，并有助于酶选择性药物设计。在此，我们采用分子动力学（MD）和量子力学/分子力学（QM/MM）相结合的方法，探索了 KDM2A 的完整催化机制，包括氧气扩散和结合、氧气活化以及底物氧化。我们的研究表明，KDM2A 的催化受第二配位层（SCS）构象变化的控制，特别是通过 Y222 取向的变化，从离线模式解锁 2OG 重排到在线模式。该研究表明，变体 Y222A 使 2OG 重排更加有利。此外，该研究表明，正是 H3K36me3 的大小阻止了 2OG 重排，从而使酶对三甲基化赖氨酸失活。计算表明，稳定 KDM2A 中 HAT 过渡态的 SCS 和长程相互作用残基与 KDM4A、KDM7B 和 KDM6A 中的不同，从而为 KDM2A 的酶选择性重新设计和调节提供了基础，而不会影响其他 KDMs。
