Introduction

Histone deacetylase 8 (HDAC8) is an enzyme that plays a role in controlling gene expression in Homo Sapiens. Specifically, HDAC8 catalyzes the removal of an acetyl group off of the ε-amino-lysine sidechain of N-terminal core of histones.^[1] Histones consist of eight monomers to form an octomer complex. Each histone has a large positive charge which allows interaction with highly negative DNA. This prevents transcription factors from accessing DNA, thus decreasing gene expression. Chromatin remodeling by histone acetylation and/or deacetylation is an example of epigenetic regulation. Histone Acetylase 1 (HAT1) catalyzes the addition of an acetyl group onto a histone. The lack of charge on the acetyl group prevents the interaction between DNA and histones. This allows transcription factors to access the DNA to increase gene expression. HDAC8 though reverses this reaction by catalyzing the removal of these acetyl groups by removing the acetate and the reclaimed positive charge on the lysine sidechain is able to interact with the negative charge on the DNA. As a result, DNA will bind more tightly to the histone protein, repressing transcription and gene expression.

HDAC Enzymes and Homology

There are four major classes of HDAC proteins (I,II, III, and IV). Other than the Class III “sirtuins” that utilize a NAD⁺ cofactor-dependent mechanism, all other HDAC classes use Zn²⁺-assisted catalysis through mechanisms reminiscent of a typical serine protease.^[2] While Classes I, II, and IV do have some major distinctions such as size of peptide, they retain a great degree of homology both between and within classes, especially at catalytic sites. HDAC 8 is among the Class I HDACs alongside HDACs 1-3. It shares a high degree of conserved residues involved in the catalytic site, Zn-binding, and ligand binding pocket (Figure 1). ^[1]

Figure 1: Nearly all active site (Asp183/H143, Asp176/His142 shown) zinc binding (Asp178 and His180 shown), and binding pocket residues (Gly151 and Phe 152 shown) are conserved across homologous sequences amongst Class I HDACs.

HDAC8 Structure

The HDAC8 comprises a single α/β domain that is composed of an eight-stranded parallel sandwiched between 13 . The HDAC8 consists of 377 amino acids, half of which are contained in the secondary structure elements and the other half are contained in loops that link the various elements of the secondary structure. The residues forming active site and catalytic machinery of the enzyme is found in the loops from the C-terminal ends of the strands of the core β-sheet. ^[3]

Zinc Ion

The pentacoordinated Zn²⁺ ion involved in the metalloenzyme catalysis is tethered to the protein through interactions with . This positions the metal ion to favorably interact with the catalytic water and acetylated lysine substrate. ^[1] The zinc ion lowers the pKa of a water proton that makes the water more nucleophilic. Besides increasing the nucleophilicity of the zinc, the zinc likely also facilitates the deacetylation process by reducing the entropy of the reaction by binding both the nucleophile and the substrate and polarizing the carbonyl of the acetyl-lysine and stabilizing the transition state.^[3]

Key Residues

The of HDAC8 is composed of 2 catalytic dyads: , which activate the catalytic water nucleophile (Figure 2). A Tyr306, through mutation to Phe in the pdb file 2v5w (modeled in the overall view) was observed to render the protein mostly inactive. Thus, it has been hypothesized that the this residue is critical for stabilization of the transition state with the Zn²⁺ ion.

Figure 2: HDAC8 utilizes a "catalytic dyad" of Asp and His. The His then assists in the coordination of the H₂O nucleophile. This mechanism is reminiscent to the catalytic triad of Asp-His-Ser in many serine proteases (with H₂O replacing the serine residue.

Binding Pocket

By encasing, the nonpolar 4 carbon-long side chain of the Lys residue on the ligand, Phe152 and Phe208 engage in hydrophobic Van der Waals with the ligand and at different ends of the , Trp141 and Met274 contribute to the overall shape through general hydrophobic interactions.^[4] Finally, the carbonyl oxygen of Gly151 hydrogen bonds with the amide hydrogen of the acetylated lysine to further interact with the ligand in the relatively hydrophobic tunnel.^[1]

Asp 101

At the rim of the active site, is involved in two hydrogen bonds between its own carbonyl oxygens and two consecutive amide hydrogens of incoming . This forces the ligand to assume a cis-conformation. In addition, extensive interactions among many other polar atoms near the rim of the active site help keep the ligand lodged in the hydrophobic tunnel.^[1]

Additional Features

Active site loop

(amino acid residues 30-36) lines a large portion of one face of the active site pocket and extends to the protein surface. This results in a larger surface opening of the active site pocket. It is suggested that this loop has high flexibility, making the active site pocket opening highly malleable and able to change to accommodate binding to a variety of different ligands. ^[3]

Ser 39

The has been shown to play a role in the activity of HDAC8 as the HDAC8 activity is regulated by phosphorylation at Ser39 by protein kinase A. The phosphorylation of Ser39 leads to a decrease in the enzyme's activity. Ser39 lies at the surface of HDAC8, roughly 20 Å from the opening to the HDAC8 active site and it could be forming part of the surface that interacts with the target histone. The phosphorylation of Ser39 could disrupt the interaction between HDAC8 and the target histone. In addition, the phosphorylated Ser39 provokes a structural rearrangement near the active site by interacting with structural elements as Lys36, part of the conformational active loop L1, that extends into the active site. The Ser39 phosphorylation could therefore be inducing a conformation of the L1 loop that prohibits a competent substrate binding. ^[3]

Mechanism

Once the substrate is bound to the binding pocket through interactions with , the water molecule nucleophilically attacks the carbonyl carbon of the ε-amino-lysine sidechain of N-terminal core of histone proteins (Figure 3). This water molecule is recruited and stabilized by . The first dyad consists of His143 and Asp183. Asp183 interacts with His143 to shift electron density so that His143 may act as a general base to remove a proton from water. The second catalytic dyad consists of His142 and Asp176 and stabilizes the now deprotonated water molecule. A Zn²⁺ ion also makes the water more acidic making it a better nucleophile. The tetrahedral intermediate is stabilized by the Zn²⁺ ion as well as Tyr306. The amine group of the histones lysine residue acts as a general base and deprotonates His143. This drives the tetrahedral intermediate to collapses and expel the acetyl group to produce an acetate ion and a deacetylated lysine residue. ^[5]

Figure 3: HDAC8 Mechanism

Medical Relevance

Besides controlling the gene regulation through deacetylation of histones, HDAC 8 also regulates the post-transcriptional acetylation status of many non-histone proteins, including transcription factors, chaperones, hormone receptors and signaling molecules. Thus, it has influences on protein stability, protein-protein interactions and protein-DNA interactions. HDAC 8 can therefore affect the regulation of cell proliferation and cell death. These processes are typically being altered in cancer cells and that makes HDAC enzymes an interesting potential target for cancer drugs. HDAC inhibitors have been shown to be promising cancer drug agents in prior research as the HDAC inhibitors cease tumor growth in cancer cells by either making them differentiate, undergo apoptosis or upregulate cell cycle arrest proteins. ^[6] One way, the HDAC inhibitors ceases tumor growth is by the reactivation of the transcription factor, RUNX3, a known tumor suppressor. HDACi increases the acetylation of the protein and as the stability of RUNX3 is dependent on the acetylation status of the protein, the increased acetylation or HDAC inhibition will enhance the protein stability, causing an increase in the anti-tumorous properties of the protein. A number of HDAC inhibitors have been purified from natural sources or synthesized and at least four structurally different inhibitor classes have been characterized: hydrox-amates, cyclic peptides, aliphatic acids and ben-zamides. The Vorinostat(within the hydroxamate class) has been FDA-approved for treatment of cancer. The hydroxamate HDAC inhibitors consists of a metal-binding domain, a linker domain and a hydrophobic capping group. The HDAC class 1 hydroxamic acid, compound 1, in a bidendate fashion while making hydrogen bonds to important residues as at the active site of HDAC8. Thus, the HDAC inhibitors can be used as antagonists to prevent the functioning of HDAC8 in cancer treatment. ^[7]