Human histone demethylase LSD1 reads the histone code

J Biol Chem. 2005 Dec 16;280(50):41360-5. doi: 10.1074/jbc.M509549200. Epub 2005 Oct 13.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Catalysis
  • Chromatin / chemistry
  • Chromatin / metabolism
  • Chromatography, Gel
  • Dose-Response Relationship, Drug
  • Enzyme Inhibitors / pharmacology
  • Epigenesis, Genetic
  • Escherichia coli / metabolism
  • Flavins / chemistry
  • Histone Demethylases
  • Histones / chemistry*
  • Humans
  • Hydrogen-Ion Concentration
  • Ions
  • Kinetics
  • Lysine / chemistry
  • Methylation
  • Models, Biological
  • Models, Chemical
  • Models, Genetic
  • Molecular Sequence Data
  • Monoamine Oxidase / chemistry
  • Oxidoreductases, N-Demethylating / metabolism
  • Oxidoreductases, N-Demethylating / physiology*
  • Peptides / chemistry
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Serine / chemistry
  • Static Electricity
  • Substrate Specificity
  • Time Factors

Substances

  • Chromatin
  • Enzyme Inhibitors
  • Flavins
  • Histones
  • Ions
  • Peptides
  • Recombinant Proteins
  • Serine
  • Histone Demethylases
  • Monoamine Oxidase
  • KDM1A protein, human
  • Oxidoreductases, N-Demethylating
  • Lysine