Molecule of the Month: Histone Deacetylases
Histone deacetylases regulate access to genetic information by modifying histones
The Deacetylation Supervisor
Working as a Team
Exploring the Structure
HDAC8 with Substrate and Inhibitors
Various HDAC inhibitors are currently being used as anticancer drugs. They act by mimicking the natural target of HDACs: an acetylated lysine amino acid. PDB ID 2v5w shows how HDAC8 recognizes the lysine. A zinc ion coordinates the acetyl group (in yellow), positioning the molecule next to several amino acids (shown in magenta here) and a water molecule (turquoise) that help with the deacetylation reaction. The inhibitors have a chemical group that mimics both the acetyl group and the water, clamping the molecule tightly to the zinc ion, as seen in the structure of trichostatin A (PDB ID 1t64), a natural product isolated from Streptomyces hygroscopicus, and the US-FDA approved anticancer drug Vorinostat (PDB ID 1t69). To explore these structures in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- You can use the structure comparison tool to explore the similarities and differences between different HDACs, such as HDAC6 (5edu), HDAC7 (3c10), and HDAC8 (1t64).
- The histone tails are very flexible, so coordinates for them are not usually included in the atomic coordinate files stored in the PDB. You can use the sequence view to determine what parts of the protein are represented in each PDB files, for example, the page for histone H3.2. Take a look at PDB ID 1kx5 for a particularly complete structure.
September 2023, Jessica Damanski, Paloma Munguía Salazar, Mihika Shah, Rajiv Snape, David S. Goodsell, Stephen K. Burleyhttp://doi.org/10.2210/rcsb_pdb/mom_2023_9