Insights into the activation mechanism of class I HDAC complexes by inositol phosphates
Open accessAbstract
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.
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D100 is a conserved class I HDAC residue that interacts with the backbone of incoming acetylated peptides.
“a conserved class I HDAC residue that has been shown to interact with the backbone of incoming acetylated peptides 33, 38”
From Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants (2018) · cites this paper as [38]
The Results section, “A novel peptide-based inhibitor mimics substrate binding” (page unavailable), reports that the conserved HDAC1 residue D99 contacts peptide-backbone amides. It does not identify that residue as D100, and the peptide used to observe the contacts was a hydroxamic-acid substrate mimic rather than an acetylated peptide. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIn hHDAC1 and hHDAC3, the corresponding arginine is involved in inositol phosphate binding and is important for activity.
“In hHDAC1 and hHDAC3 this arginine is involved in inositol phosphate binding and is important for activity 38, 47, 48 .”
From Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants (2018) · cites this paper as [38]
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- Authors
- Watson, P. J., Millard, C. J., Riley, A. M., Robertson, N. S., Wright, L. C., Godage, H. Y., Cowley, S. M., Jamieson, A. G., Potter, B. V. L., & Schwabe, J. W. R.
- Affiliations
- University of Leicester (GB)
- University of Bath (GB)
- University of Oxford (GB)
- Corresponding author
- Schwabe, John W. R.
- ORCID
- Venue
- Nature Communications
- Published
- 2016-04-25
- Volume
- 7
- Issue
- 1
- Pages
- 11262-11262
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC4848466
- OpenAlex
- W2320230258
- Cited by
- 244
- References
- 68
- Citations by year
- 2026: 21 · 2025: 23 · 2024: 24 · 2023: 30 · 2022: 21 · 2021: 28 · 2020: 27 · 2019: 31 · 2018: 22 · 2017: 12 · 2016: 4 · 2013: 1
- FWCI
- 12.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- Leicester Research Archive (University of Leicester) (acceptedVersion, cc-by)
- The University of Bath Online Publications Store (The University of Bath) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Leicester Research Archive (University of Leicester) (submittedVersion, cc-by)
- Pure (University of Bath) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (100237/Z/12/Z, 101010/B/13/Z, WT085408, WT082837, WT100237)
- Diamond Light Source
- Medical Research Council (MC_PC_14117, MR/J009202/1)
- Biotechnology and Biological Sciences Research Council (BB/J009598/1, BB/N002954/1, 1752770)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- histone deacetylase, HDAC1, inositol phosphates, phytic acid, allosteric activation, allosteric communication, substrate recognition, peptide inhibitors, crystal structure
- MeSH terms
- Protein Domains, Histone Deacetylase 3, Allosteric Regulation, Binding Sites, Enzyme Activation, Histone Deacetylases, Humans, Inositol Phosphates, Protein Binding, Crystallography, X-Ray, Catalytic Domain, Multiprotein Complexes, Histone Deacetylase 1, HEK293 Cells, Molecular Docking Simulation
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