A rationally-designed chimeric KDM1A/KDM1B histone demethylase tower domain deletion mutant retaining enzymatic activity

• A KDM1A/KDM1B chimera was engineered to omit the protein-interacting tower domain.
• The enzymatically active chimera copurifies with a stoichiometric equivalent of FAD.
• The KDM1A tower domain is non-essential for demethylase activity in vitro.
• The chimera fails to bind CoREST, decoupling activity from tower-dependent binding.
• This mutant is a tool to study the impact of protein interactions on KDM1A function.

A target with therapeutic potential, lysine-specific demethylase 1A (KDM1A) is a regulator of gene expression whose tower domain is a protein–protein interaction motif. This domain facilitates the interaction of KDM1A with coregulators and multiprotein complexes that direct its activity to nucleosomes. We describe the design and characterization of a chimeric ‘towerless’ KDM1A, termed nΔ150 KDM1AΔTower KDM1B chimera (chKDM1AΔTower), which incorporates a region from the paralog lysine-specific demethylase 1B (KDM1B). This chimera copurifies with FAD and displays demethylase activity, but fails to bind the partner protein corepressor of the RE1-silencing transcription factor (CoREST). We conclude that KDM1A catalysis can be decoupled from tower-dependent interactions, lending chKDM1AΔTower useful for dissecting molecular contributions to KDM1A function.