title: Structural insights into HDAC6 tubulin deacetylation and its selective inhibition.
abstract: 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.
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Miyake
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Keusch
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
authors.forename: Longlong
authors.initials: L
authors.lastname: Wang
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
authors.forename: Makoto
authors.initials: M
authors.lastname: Saito
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Hess
authors.affiliation: Department of Chemistry &Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
authors.forename: Xiaoning
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Chemistry &Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Melancon
authors.affiliation: Department of Chemistry &Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Helquist
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
authors.forename: Heinz
authors.initials: H
authors.lastname: Gut
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.|Faculty of Sciences, University of Basel, Basel, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Matthias
mesh_terms: D000107:Acetylation / Q000187:drug effects; D000818:Animals; D055162:Biocatalysis; D000073864:Histone Deacetylase 6; D056572:Histone Deacetylase Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D006655:Histone Deacetylases / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D006877:Hydroxamic Acids / Q000737:chemistry / Q000494:pharmacology*; D008958:Models, Molecular; D013329:Structure-Activity Relationship; D014404:Tubulin / Q000737:chemistry / Q000378:metabolism*; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*
chemical_list: D056572:Histone Deacetylase Inhibitors; D006877:Hydroxamic Acids; D014404:Tubulin; D029961:Zebrafish Proteins; C012589:trichostatin A; C433811:HDAC6 protein, human; C568523:HDAC6 protein, zebrafish; D000073864:Histone Deacetylase 6; D006655:Histone Deacetylases