A distal regulatory region of a class I human histone deacetylase

Abstract

Histone deacetylases (HDACs) are key enzymes in epigenetics and important drug targets in cancer biology. Whilst it has been established that HDACs regulate many cellular processes, far less is known about the regulation of these enzymes themselves. Here, we show that HDAC8 is allosterically regulated by shifts in populations between exchanging states. An inactive state is identified, which is stabilised by a range of mutations and resembles a sparsely-populated state in equilibrium with active HDAC8. Computational models show that the inactive and active states differ by small changes in a regulatory region that extends up to 28 Å from the active site. The regulatory allosteric region identified here in HDAC8 corresponds to regions in other class I HDACs known to bind regulators, thus suggesting a general mechanism. The presented results pave the way for the development of allosteric HDAC inhibitors and regulators to improve the therapy for several disease states.

FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling

“…HDAC8: A 2D 13 C- 1 H HMQC methyl-TROSY correlation spectrum was recorded on a methyl-labelled (isoleucine, leucine and valine methyl groups are isotopically 13 C- 1 H labelled with specific pro-(S) labelling for leucine and valine groups) HDAC8 sample, prepared according to previously reported protocols (Werbeck et al 2020 ). The spectrum was recorded at 298 K on an NMR spectrometer operating at 800 MHz 1 H Larmor frequency and equipped with a helium-cooled TCI inverse cryoprobe.…”

FID-Net: A Versatile Deep Neural Network Architecture for NMR Spectral Reconstruction and Virtual Decoupling

“…HDAC8: A 2D 13 C-1 H HMQC methyl-TROSY correlation spectrum was recorded on a methyllabelled (isoleucine, leucine and valine methyl groups are isotopically 13 C-1 H labelled with specific pro-(S) labelling for leucine and valine groups) HDAC8 sample, prepared according to previously reported protocols 33 . The spectrum was recorded at 298 K on an NMR spectrometer operating at 800 MHz 1 H Larmor frequency and equipped with a helium-cooled TCI inverse cryoprobe.…”

Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8

“…In contrast, HDAC8 has a regulatory serine phosphorylation site at position 39, in the catalytic domain, and its phosphorylation inactivates the enzyme by stabilising an inactive state. 2,17 Recently, in HDAC1, HDAC2, and HDAC3, the region corresponding to the S39 site in HDAC8 was shown to act as a binding platform in holoenzyme HDAC complexes, suggesting a general mechanism for regulation across class I HDACs. [17][18][19][20] The overall fold of HDAC8, as observed in substrate-and inhibitor-HDAC8 complexes, is comprised of an eight stranded b-sheet, which is surrounded by 11 helices and two helical turns.…”

“…2,17 Recently, in HDAC1, HDAC2, and HDAC3, the region corresponding to the S39 site in HDAC8 was shown to act as a binding platform in holoenzyme HDAC complexes, suggesting a general mechanism for regulation across class I HDACs. [17][18][19][20] The overall fold of HDAC8, as observed in substrate-and inhibitor-HDAC8 complexes, is comprised of an eight stranded b-sheet, which is surrounded by 11 helices and two helical turns. [21][22][23][24][25][26] The active site is formed by seven loops, L1 to L7, connecting these secondary structure elements.…”

“…The F152 side chain samples the gaucheÀ (c 1 z 300 ; gÀ) and the trans (c 1 z 200 ; t) states each with an average life-time of about 1 ns. (b) Two-dimensional histogram showing that the c 1 dihedral angle of F152 correlates strongly with the distance between K33 C a within the L1 loop and F152 C a ; a distance which has previously been used as a measure of the L1 conformation 17. (c) Two-dimensional histogram showing that the distance between the side chains of K33 in L1 and D87 in L2 as well as ability to form a salt-bridge between the two side chains, correlate with the c 1 of F152.…”