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Histone deacetylase 6 structure and molecular basis of catalysis and inhibition

Abstract

Histone deacetylase 6 (HDAC6) is a critical target for drug design because of its role in oncogenic transformation and cancer metastasis, and is unique among all histone deacetylases in that it contains tandem catalytic domains designated CD1 and CD2. We now report the crystal structures of CD2 from Homo sapiens HDAC6 and of CD1 and CD2 from Danio rerio HDAC6. We correlated these structures with activity measurements using 13 different substrates. The catalytic activity of CD2 from both species exhibited broad substrate specificity, whereas that of CD1 was highly specific for substrates bearing C-terminal acetyllysine residues. Crystal structures of substrate complexes yielded unprecedented snapshots of the catalytic mechanism. Additionally, crystal structures of complexes with eight different inhibitors, including belinostat and panobinostat (currently used in cancer chemotherapy), the macrocyclic tetrapeptide HC toxin, and the HDAC6-specific inhibitor N-hydroxy-4-(2-((2-hydroxyethyl)(phenyl)amino)-2-oxoethyl)benzamide, revealed surprising new insight regarding changes in Zn2+ coordination and isozyme-specific inhibition.

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Figure 1: Human and zebrafish HDAC6 domains and activity.
Figure 2: Snapshots of catalysis by HDAC6 zCD2.
Figure 3: Peptide binding to zCD2 exemplified by substrates and HC toxin.
Figure 4: Structural basis of CD1 substrate specificity.
Figure 5: Inhibitor binding to zCD2.

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Acknowledgements

We thank R. Marmorstein, B.S. Cooperman, X. Li, and M. Chen for helpful discussions, the National Institutes of Health (NIH) for grant GM49758 to D.W.C. in support of this research, and V. Stojanoff, D. Neau, and J. Nix for assistance with synchrotron data collection. For synchrotron access, we are grateful to the Northeastern Collaborative Access Team beamline 24-ID-E at the Advanced Photon Source, Argonne National Laboratory; the Structural Molecular Biology Program beamline 14-1 at the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory; and the Molecular Biology Consortium beamline 4.2.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory. Finally, D.W.C. thanks the Radcliffe Institute for Advanced Study at Harvard University for the Elizabeth S. and Richard M. Cashin Fellowship.

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Y.H. and D.W.C. designed the project. Y.H. performed experiments. Y.H. and D.W.C. interpreted experimental results and prepared the manuscript.

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Correspondence to David W Christianson.

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Hai, Y., Christianson, D. Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat Chem Biol 12, 741–747 (2016). https://doi.org/10.1038/nchembio.2134

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