5BWZ

Crystal structure of S39E HDAC8 in complex with Droxinostat

Summary for 5BWZ

• Entry DOI: 10.2210/pdb5bwz/pdb
• Descriptor: Histone deacetylase 8, ZINC ION, POTASSIUM ION, ... (6 entities in total)
• Functional Keywords: arginase/deacetylase fold, hydrolase, histone deacetylase, enzyme inhibitor-complex, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 87414.73

Authors

Decroos, C.,Christianson, D.W. (deposition date: 2015-06-08, release date: 2016-06-08, Last modification date: 2023-09-27)

Primary citation

Welker Leng, K.R.,Castaneda, C.A.,Decroos, C.,Islam, B.,Haider, S.M.,Christianson, D.W.,Fierke, C.A.
Phosphorylation of Histone Deacetylase 8: Structural and Mechanistic Analysis of the Phosphomimetic S39E Mutant.
Biochemistry, 58:4480-4493, 2019

PubMed Abstract: Histone deacetylase (HDAC) enzymes that catalyze removal of acetyl-lysine post-translational modifications are frequently post-translationally modified. HDAC8 is phosphorylated within the deacetylase domain at conserved residue serine 39, which leads to decreased catalytic activity. HDAC8 phosphorylation at S39 is unique in its location and function and may represent a novel mode of deacetylation regulation. To better understand the impact of phosphorylation of HDAC8 on enzyme structure and function, we performed crystallographic, kinetic, and molecular dynamics studies of the S39E HDAC8 phosphomimetic mutant. This mutation decreases the level of deacetylation of peptides derived from acetylated nuclear and cytoplasmic proteins. However, the magnitude of the effect depends on the peptide sequence and the identity of the active site metal ion [Zn(II) vs Fe(II)], with the value of / for the mutant decreasing 9- to >200-fold compared to that of wild-type HDAC8. Furthermore, the dissociation rate constant of the active site metal ion increases by ∼10-fold. S39E HDAC8 was crystallized in complex with the inhibitor Droxinostat, revealing that phosphorylation of S39, as mimicked by the glutamate side chain, perturbs local structure through distortion of the L1 loop. Molecular dynamics simulations of both S39E and phosphorylated S39 HDAC8 demonstrate that the perturbation of the L1 loop likely occurs because of the lost hydrogen bond between D29 and S39. Furthermore, the S39 perturbation causes structural changes that propagate through the protein scaffolding to influence function in the active site. These data demonstrate that phosphorylation plays an important regulatory role for HDAC8 by affecting ligand binding, catalytic efficiency, and substrate selectivity.

PubMed: 31633931
DOI: 10.1021/acs.biochem.9b00653

Experimental method

X-RAY DIFFRACTION (1.59 Å)