Human histone demethylase LSD1 reads the histone code.
Human histone demethylase LSD1 is a flavin-dependent amine oxidase that catalyzes the specific removal of methyl groups from mono- and dimethylated Lys4 of histone H3. The N-terminal tail of H3 is subject to various covalent modifications, and a fundamental question in LSD1 biology is how these epigenetic marks affect the demethylase activity. We show that LSD1 does not have a strong preference for mono- or dimethylated Lys4 of H3. Substrate recognition is not confined to the residues neighboring Lys4, but it requires a sufficiently long peptide segment consisting of the N-terminal 20 amino acids of H3. Electrostatic interactions are an important factor in protein-substrate recognition, as indicated by the high sensitivity of Km to ionic strength. We have probed LSD1 for its ability to demethylate Lys4 in presence of a second modification on the same peptide substrate. Methylation of Lys9 does not affect enzyme catalysis. Conversely, Lys9 acetylation causes an almost 6-fold increase in the Km value, whereas phosphorylation of Ser10 totally abolishes activity. LSD1 is inhibited by a demethylated peptide with an inhibition constant of 1.8 microM, suggesting that LSD1 can bind to H3 independently of Lys4 methylation. LSD1 is a chromatin-modifying enzyme, which is able to read different epigenetic marks on the histone N-terminal tail and can serve as a docking module for the stabilization of the associated corepressor complex(es) on chromatin.
Forneris
Federico
F
Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Ferrata 1, Pavia 27100, Italy.
Binda
Claudia
C
Vanoni
Maria Antonietta
MA
Battaglioli
Elena
E
Mattevi
Andrea
A
D000595:Amino Acid Sequence; D002384:Catalysis; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D002850:Chromatography, Gel; D004305:Dose-Response Relationship, Drug; D004791:Enzyme Inhibitors / Q000494:pharmacology; D044127:Epigenesis, Genetic; D004926:Escherichia coli / Q000378:metabolism; D005415:Flavins / Q000737:chemistry; D056466:Histone Demethylases; D006657:Histones / Q000737:chemistry*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007477:Ions; D007700:Kinetics; D008239:Lysine / Q000737:chemistry; D008745:Methylation; D008954:Models, Biological; D008956:Models, Chemical; D008957:Models, Genetic; D008969:Molecular Sequence Data; D008995:Monoamine Oxidase / Q000737:chemistry; D010089:Oxidoreductases, N-Demethylating / Q000378:metabolism / Q000502:physiology*; D010455:Peptides / Q000737:chemistry; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry; D012694:Serine / Q000737:chemistry; D055672:Static Electricity; D013379:Substrate Specificity; D013997:Time Factors
D002843:Chromatin; D004791:Enzyme Inhibitors; D005415:Flavins; D006657:Histones; D007477:Ions; D010455:Peptides; D011994:Recombinant Proteins; D012694:Serine; D056466:Histone Demethylases; D008995:Monoamine Oxidase; C495195:KDM1A protein, human; D010089:Oxidoreductases, N-Demethylating; D008239:Lysine