5ICN

HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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.Schwabe, J.W.

(2016) Nat Commun 7: 11262-11262

  • DOI: 10.1038/ncomms11262

  • PubMed 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 bi ...

    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.


    Organizational Affiliation

    Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, UK.,Department of Pharmacy and Pharmacology, University of Bath BA2 7AY, UK.,Department of Chemistry, University of Leicester, Leicester LE1 7RH, UK.,Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metastasis-associated protein MTA1
A
195Homo sapiensMutation(s): 0 
Gene Names: MTA1
Find proteins for Q13330 (Homo sapiens)
Go to Gene View: MTA1
Go to UniProtKB:  Q13330
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 1
B
376Homo sapiensMutation(s): 0 
Gene Names: HDAC1 (RPD3L1)
EC: 3.5.1.98
Find proteins for Q13547 (Homo sapiens)
Go to Gene View: HDAC1
Go to UniProtKB:  Q13547
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GLY-ALA-6A0-ARG-HIS
C
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
I6P
Query on I6P

Download SDF File 
Download CCD File 
A
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
MYO-INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6A0
Query on 6A0
C
NON-POLYMERC8 H16 N2 O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.815α = 90.00
b = 107.815β = 90.00
c = 134.161γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT085408
Wellcome TrustUnited KingdomWT100237
Wellcome TrustUnited KingdomWT082837
Wellcome TrustUnited KingdomWT101010
Wolfson FoundationUnited Kingdom--

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy