Insights into the activation mechanism of class I HDAC complexes by inositol phosphates.

Peter J Watson,John W R Schwabe,Barry V L Potter,Himali Y Godage,Christopher J Millard,Naomi S Robertson,Andrew M Riley,Andrew G Jamieson,Shaun M Cowley,Lyndsey C Wright

doi:10.1038/ncomms11262

Abstract

Histone deacetylases (HDACs) 1, 2 and 3 form the catalytic subunit of several large transcriptional repression complexes. Unexpectedly, the enzymatic activity of HDACs in these complexes has been shown to be regulated by inositol phosphates, which bind in a pocket sandwiched between the HDAC and co-repressor proteins. However, the actual mechanism of activation remains poorly understood. Here we have elucidated the stereochemical requirements for binding and activation by inositol phosphates, demonstrating that activation requires three adjacent phosphate groups and that other positions on the inositol ring can tolerate bulky substituents. We also demonstrate that there is allosteric communication between the inositol-binding site and the active site. The crystal structure of the HDAC1:MTA1 complex bound to a novel peptide-based inhibitor and to inositol hexaphosphate suggests a molecular basis of substrate recognition, and an entropically driven allosteric mechanism of activation.

Highlights

Histone deacetylases (HDACs) 1, 2 and 3 form the catalytic subunit of several large transcriptional repression complexes
To understand the stereochemical basis underlying the activation of HDAC3 by inositol phosphates we investigated the ability of a range of inositol phosphates and derivatives to enhance the activity of HDAC3 in deacetylase assays
To achieve this we used an assay based on the complex of HDAC3 with an extended SMRT construct which is stable in the absence of inositol phosphate3

Summary

Introduction

Histone deacetylases (HDACs) 1, 2 and 3 form the catalytic subunit of several large transcriptional repression complexes. The enzymatic activity of HDACs in these complexes has been shown to be regulated by inositol phosphates, which bind in a pocket sandwiched between the HDAC and co-repressor proteins. HDAC3, is exclusively recruited to the SMRT/NCoR co-repressor complex20,27 The regulation of these complexes by inositol phosphates was first suggested by the surprising discovery that inositol 1,4,5,6-tetrakisphosphate (Ins[1,4,5,6]P4) was present in the HDAC3:SMRT crystal structure. The key residues which coordinate the binding of Ins[1,4,5,6]P4 to the HDAC3:SMRT complex were found to be conserved in several class I HDAC complexes, suggesting that these complexes may be activated by inositol phosphates. The novel MiDAC complex has been shown to be activated by exogenous Ins[1,4,5,6]P4 (ref. 4)

Methods

Results

Conclusion