A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions

Abstract

Zinc-dependent histone deacetylase 8 (HDAC8) catalyzes the removal of acetyl moieties from histone tails, and is critically involved in regulating chromatin structure and gene expression. The detailed knowledge of its catalytic process is of high importance since it has been established as a most promising target for the development of new anti-tumor drugs. By employing BornOppenheimer ab initio QM/MM molecular dynamics simulations and umbrella sampling, a stateof-the-art approach to simulate enzyme reactions, we have provided further evidences against the originally proposed general acid-base catalytic pair mechanism for Zinc-dependent histone deacetylases. Instead, our results indicated that HDAC8 employs a proton-shuttle catalytic mechanism, in which a neutral His143 first serves as the general base to accept a proton from the zinc-bound water molecule in the initial rate-determining nucleophilic attack step, and then shuttles it to the amide nitrogen atom to facilitate the cleavage of the amide bond. During the deacetylation process, the Zn 2+ ion changes its coordination mode and plays multiple catalytic roles. For the K + ion, which is located about 7 Å from the catalytic Zn 2+ ion and conserved in class I and II HDACs, our simulations indicated that its removal would lead to the different transition state structure and a higher free energy reaction barrier for the rate-determining step. It is found that the existence of this conserved K + ion would enhance the substrate binding, increase the basicity of His143, strengthen the catalytic role of zinc ion and improve the transition state stabilization by the enzyme environment.

Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions

“…It is a common strategy to prevent the collapse of the coordinate structures. 64,65 To check whether this scheme will influence the active-site structures of the two QueE−substrate complexes, we also performed 5 ns MD simulations without fixing the positions of Mg 2+ and Na + . The MD simulations …”

Structural insight into the separate roles of inositol tetraphosphate and deacetylase‐activating domain in activation of histone deacetylase 3

“…2(C)]. The DAD domain, on the other hand, has a more notable stabilizing effect on Loop 1 (residues [19][20][21][22][23][24][25]. Neither the binding of DAD nor IP4 appears to affect the random coil at residues 340-348 substantially, but the binding of both corepressors does seem to cause an increase in flexibility in this region.…”

Expression, purification, and <i>S</i>-nitrosylation of recombinant histone deacetylase 8 in <i>Escherichia coli </i>

“…Generally, the Zn 2+ -dependent HDACs are more important to modulate transcription and gene expression, and most HDAC inhibitors are designed to act on these HDACs (5). The zinc-dependent HDAC8 catalyzes the removal of acetyl moieties from histone tails, and is critically involved in regulating chromatin structure and gene expression (6). Recently, it was reported that HDAC8-selective inhibitors are available, and HDAC8 may be a potential drug target for neuroblastoma differentiation therapy using selective inhibitors, avoiding nonspecific side effects (7).…”