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.