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Structures of ‘hot’ cancer target solved

Knowing HDAC6’s configuration could help researchers design therapeutics

by Celia Henry Arnaud
July 27, 2016 | APPEARED IN VOLUME 94, ISSUE 31

Credit: Nat. Chem. Biol.
CD1 (blue) and CD2 (dark red) form an ellipsoid complex with pseudo-twofold symmetry. The linker (green) connecting the two domains is on the outside of the complex. Metal ions are gray spheres. Red arrows indicate the position of the substrate binding cleft in each domain.

The enzyme HDAC6 is a “sizzling hot target for cancer chemotherapy,” says David W. Christianson, a chemist at the University of Pennsylvania who studies the enzyme. More formally known as histone deacetylase 6, this enzyme is responsible for removing acetyl groups from the protein tubulin, a structural component of a cell’s inner scaffold. Interfering with this deacetylation process can disrupt a cell’s ability to divide and transport nutrients, leading ultimately to cell death.

¡Te tengo!
Credit: Nat. Chem. Biol.
Sustituyendo una histidina involucrada en catálisis por una alanina (H574A), Christianson y Hai pudieron atrapar un intermedio tetraédrico de la reacción de desacetilación en el sitio activo CD2 de HDAC6. Crédito: Nat. Chem. Biol.
Credit: Nat. Chem. Biol.
By substituting a histidine involved in catalysis with an alanine (H574A), Christianson and Hai were able to trap a tetrahedral intermediate of the deacetylation reaction in the CD2 active site of HDAC6.

Because researchers would like to disrupt tumor cells this way, they’ve been looking for HDAC6 inhibitors as potential cancer treatments. So far, they have needed to search in the dark without a crystal structure to guide them—but not anymore.

Now two independent groups have solved structures of HDAC6 from zebrafish. Christianson and graduate student Yang Hai solved one set of crystal structures (Nat. Chem. Biol. 2016, DOI: 10.1038/nchembio.2134).They also solved one structure of human HDAC6, which showed that the zebrafish version is a suitable surrogate. The other set was solved by Patrick Matthias of the Friedrich Miescher Institute for Biomedical Research and coworkers (Nat. Chem. Biol. 2016, DOI: 10.1038/nchembio.2140).

Unlike other histone deacetylases, HDAC6 has two domains that catalyze acetyl group removal. Catalytic domain 2 (CD2) is the main site for deacetylation. Catalytic domain 1 (CD1), in contrast, is often called the “low activity” or “no activity” domain.

Christianson and Hai learned that, contrary to its nickname, CD1 can be quite active with the right substrate. CD1 has a lysine residue in its binding site where CD2 has a leucine. Using peptide substrates to model segments of tubulin, the researchers learned that CD1’s lysine serves as a “gatekeeper” that blocks the active site from all substrates except those that have an acetylated lysine at their carboxy terminus. The researchers aren’t yet sure why CD1 has that specificity in terms of its regulation of tubulin, Christianson says.

The team, however, was able to get snapshots of HDAC6’s catalytic mechanism. By replacing a histidine in the enzyme’s active site, the researchers were able to trap a tetrahedral intermediate of the deacetylation reaction. They also solved structures of HDAC6 with various substrates and inhibitors.

Both groups solved structures of the isolated catalytic domains. In addition, Matthias’s group solved a structure of CD1 and CD2 linked to one another. Together, the domains take on an ellipsoid shape with pseudo-twofold symmetry. “There is a large area of interaction between the two domains, with the linker on the outside,” Matthias says.

In addition, Matthias’s team found that HDAC6 gets its specificity for tubulin from a helix that is oriented differently than in other HDACs and from a flexible tryptophan in a loop connecting two of the enzyme’s helices.

“Both the Matthias and Christianson papers determine enzyme-inhibitor structures useful for pushing therapeutic discovery forward,” says Karen N. Allen, an enzyme researcher at Boston University. “These papers are chock-full of important information.”

This article has been translated into Spanish by and can be found here.



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