Human Deacetylase Protein HDAC8

Seryne Rafique '26 and Anjali Zumkhawala-Cook '26

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I. Introduction

HDAC8 is an enzyme in the family of histone deacetylases, which work to regulate gene expression. By catalyzing the removal of a lysine at the N termini of histones, HDAC8 limits transcriptive machinery from accessing the genome, thus epigenetically repressing genes. HDAC8 interacts primarily with the H3 and H4 the domains of histones and facilitates an attack on the acetyl group by water at the N-terminus lysine. Specific lysines are sites of reversible acetylation, which enhances histone deacetylases ability to regulate gene expression (Khochbin).

Regulation of histone activity is of particular interest in cancer biologyas its regulation can lead to the expression or regulation of key cancer causing genes. Its wide usage in the genome contributes to therapeutic uses that relate to regulation of cell differentiation, cell cycle arrest, and tumor growth suppression. 

II. General Structure

HDAC8 contains a αβ domain including eight stranded beta sheets embedded in 13 α helices. Much of the protein's volume is made up by the loops off of the β sheet strands which also surround the active site machinery. Class I histone deacetylases are recognized for their well conserved catalytic domains (Khochbin).

A distinguishing feature of the structure of HDAC8 is the absence of a 50-111 amino acid C-terminal domain extending from the catalytic domain. Compared to other class I histone deacetylase, HDAC8 ends at This means that either HDAC8 does not require recruitment to protein complexes or that its recruitment relies on different regions altogether. Similar to other class I HDACs, HDAC8 has a long fatty acid chain that is accommodated in an internal pocket. However it is associated with weak fatty acid deacetylase activity (Porter NJ).

Another feature that distinguishes HDAC8 from other class I enzymes is that the N-terminal in HDAC8 is two residues shorter, resulting in a wider active site pocket and larger surface opening. This results in more flexibility of the L1 loop to accommodate a variety of ligands.

A is found in the interior of the protein by the active site and is bound by six oxygen ligands, contributed by D176, S199, and backbone carbonyl oxygens of The sodium is thought to either regulate the basicity of residues or to stabilize the active site.   

III. Active Site

The active site has long hydrophobic tunnels that lead to a cavity which possesses the catalytic machinery. These tunnels are occupied by the four methylene groups of the acetylated lysine during deacetylation reactions. Half of the residues in HDAC8 form loops from the C-terminal ends of the strands and link elements of the secondary structure to form the enzyme’s active site and catalytic machinery.

A central bound to carboxylate oxygens and functions as a coordination site for catalysis. In addition to its structural contributions, it coordinates the interaction between the acetyl group of the histone and nucleophilic attack by water, ultimately resulting in the deacetylation reaction. Zinc has the capacity to facilitate the reaction in two ways: first, by binding the nucleophile and the substrate to reduce the entropy of the reaction and second, by increasing its electrophilicity by polarizing the carbonyl of the acetyl-lysine.

The larger surface opening of the L1 loop and greater flexibility allows for the loop to peel away from the protein and expose a deep binding groove adjacent to the binding site. HDAC8 is able to expose a large second cavity even after the L1 loop moves toward the active site and positions K33 so that methylene groups pack against the F152 side chain, causing the second pocket to be occluded (Wyngaert). This suggests that HDAC8 may be able to deacetylate lysine residues even when lysine residues are inaccessible. Monomers A/D or B/C interact through the symmetric peripheral 173 flap, 97 and 60 loop. Both 97 loops on each segment experience Van der Waals forces between the Ile 99 side chains on segments 95-99 [95-99 bonds] There is additional hydrophobic interaction at the outer edge of the A/D or B/C monomer pairs between Pro 60A-Asp 60B and Gly 173B and Tyr 173D. They are also cross-linked via salt-bridges between Asp 60B and Arg224; as well as through 4 hydrogen bonds [all local linkages].

IV. Regulation

HDAC is primarily regulated by phosphorylation of by Protein Kinase A. Due to its proximity to other key residues in the active site, phosphorylation of Ser39 poses a major disruption in active site geometry. Applications of drug induced HDAC8 include the introduction of inhibitors like forms a complex with HDAC8 and occludes the active site. Note the interactions between TSA and the active site. Interestingly and as described above, the L1 loop’s unique flexibility opens up a second site for ligand binding. For this reason, a second TSA molecule is required to inhibit both sites. This characteristic must be considered when applying inhibition of HDAC8 in therapeutic contexts. 

V. Implications

Beyond the regulation of gene expression, HDACs assist in DNA repair, apoptosis, stress responses, and the oversight of the cell cycle. Class 1 HDACs are uniquely important for their ability to silence genes at key locations in nucleosomes through interacting with transcription complexes. Understanding the structure of HDAC8 specifically allows researchers to better conceptualize the way in which inhibitors function and bind from a clinical standpoint (Strul 98).

VI. References

Ilse Van den Wyngaert, Winfred de Vries, Andreas Kremer, Jean-Marc Neefs, Peter Verhasselt, Walter H.M.L. Luyten, Stefan U. Kass, Cloning and characterization of human histone deacetylase 8, FEBS Letters, Volume 478, Issues 1–2, 2000, Pages 77-83, ISSN 0014-5793, https://doi.org/10.1016/S0014-5793(00)01813-5.

Porter NJ, Christianson DW. Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases. Curr Opin Struct Biol. 2019 Dec;59:9-18. doi: 10.1016/j.sbi.2019.01.004. Epub 2019 Feb 8. PMID: 30743180; PMCID: PMC6687579.

Saadi Khochbin, André Verdel, Claudie Lemercier, Daphné Seigneurin-Berny, Functional significance of histone deacetylase diversity, Current Opinion in Genetics & Development, Volume 11, Issue 2, 2001, Pages 162-166, ISSN 0959-437X, https://doi.org/10.1016/S0959-437X(00)00174-X.

Kevin Strul, Genes & Dev. 1998. 12: 599-606 Cold Spring Harbor Laboratory Press, 96(20), pp. 10984–10991. 96.20.10984.

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