A Highly Specific Mechanism of Histone H3-K4 Recognition

Human lysine-specific demethylase (LSD1) is a chromatin-modifying enzyme that specifically removesmethyl groups from mono- and dimethylated Lys4 of histoneH3 (H3-K4).We used a combination of in vivo and in vitro experiments to characterize the substrate specificity and recognition by LSD1. Biochemical assays on histone peptides show that essentially all epigenetic modifications on the 21 N-terminal amino acids of histone H3 cause a significant reduction in enzymatic activity. Replacement of Lys4 with Arg greatly enhances binding affinity, and a histone peptide incorporating this mutation has a strong inhibitory power. Conversely, a peptide bearing a trimethylated Lys4 is only a weak inhibitor of the enzyme. Rapid kinetics measure-ments evidence that the enzyme is efficiently reoxidized by molecular oxygenwith a second-order rate constant of 9.6 103 M1 s1, and that the presence of the reaction product does no