Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes

Curr Opin Struct Biol. 2011 Dec;21(6):735-43. doi: 10.1016/ Epub 2011 Aug 25.


Metal-dependent histone deacetylases (HDACs) catalyze the hydrolysis of acetyl-L-lysine side chains in histone and nonhistone proteins to yield l-lysine and acetate. This chemistry plays a critical role in the regulation of numerous biological processes. Aberrant HDAC activity is implicated in various diseases, and HDACs are validated targets for drug design. Two HDAC inhibitors are currently approved for cancer chemotherapy, and other inhibitors are in clinical trials. To date, X-ray crystal structures are available for four human HDACs (2, 4, 7, and 8) and three HDAC-related deacetylases from bacteria (histone deacetylase-like protein (HDLP); histone deacetylase-like amidohydrolase (HDAH); acetylpolyamine amidohydrolase (APAH)). Structural comparisons among these enzymes reveal a conserved constellation of active site residues, suggesting a common mechanism for the metal-dependent hydrolysis of acetylated substrates. Structural analyses of HDACs and HDAC-related deacetylases guide the design of tight-binding inhibitors, and future prospects for developing isozyme-specific inhibitors are quite promising.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Acetylation
  • Animals
  • Catalytic Domain
  • Crystallography, X-Ray
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / metabolism
  • Histone Deacetylase Inhibitors / chemistry*
  • Histone Deacetylase Inhibitors / metabolism
  • Histone Deacetylases / chemistry*
  • Histone Deacetylases / metabolism
  • Humans
  • Lysine / genetics
  • Lysine / metabolism
  • Metalloproteins / chemistry*
  • Metalloproteins / metabolism
  • Protein Conformation


  • Enzyme Inhibitors
  • Histone Deacetylase Inhibitors
  • Metalloproteins
  • Histone Deacetylases
  • Lysine