Structural insights into HDAC6 tubulin deacetylation and its selective inhibition

Nat Chem Biol. 2016 Sep;12(9):748-54. doi: 10.1038/nchembio.2140. Epub 2016 Jul 25.


We report crystal structures of zebrafish histone deacetylase 6 (HDAC6) catalytic domains in tandem or as single domains in complex with the (R) and (S) enantiomers of trichostatin A (TSA) or with the HDAC6-specific inhibitor nexturastat A. The tandem domains formed, together with the inter-domain linker, an ellipsoid-shaped complex with pseudo-twofold symmetry. We identified important active site differences between both catalytic domains and revealed the binding mode of HDAC6 selective inhibitors. HDAC inhibition assays with (R)- and (S)-TSA showed that (R)-TSA was a broad-range inhibitor, whereas (S)-TSA had moderate selectivity for HDAC6. We identified a uniquely positioned α-helix and a flexible tryptophan residue in the loop joining α-helices H20 to H21 as critical for deacetylation of the physiologic substrate tubulin. Using single-molecule measurements and biochemical assays we demonstrated that HDAC6 catalytic domain 2 deacetylated α-tubulin lysine 40 in the lumen of microtubules, but that its preferred substrate was unpolymerized tubulin.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Acetylation / drug effects
  • Animals
  • Biocatalysis
  • Histone Deacetylase 6
  • Histone Deacetylase Inhibitors / chemistry
  • Histone Deacetylase Inhibitors / pharmacology*
  • Histone Deacetylases / chemistry
  • Histone Deacetylases / metabolism*
  • Humans
  • Hydroxamic Acids / chemistry
  • Hydroxamic Acids / pharmacology*
  • Models, Molecular
  • Structure-Activity Relationship
  • Tubulin / chemistry
  • Tubulin / metabolism*
  • Zebrafish
  • Zebrafish Proteins / antagonists & inhibitors*
  • Zebrafish Proteins / chemistry
  • Zebrafish Proteins / metabolism*


  • Histone Deacetylase Inhibitors
  • Hydroxamic Acids
  • Tubulin
  • Zebrafish Proteins
  • trichostatin A
  • HDAC6 protein, human
  • HDAC6 protein, zebrafish
  • Histone Deacetylase 6
  • Histone Deacetylases