4QA2

Crystal structure of I243N HDAC8 in complex with SAHA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders.

Decroos, C.Bowman, C.M.Moser, J.A.Christianson, K.E.Deardorff, M.A.Christianson, D.W.

(2014) ACS Chem Biol 9: 2157-2164

  • DOI: https://doi.org/10.1021/cb5003762
  • Primary Citation of Related Structures:  
    4QA0, 4QA1, 4QA2, 4QA3, 4QA4, 4QA5, 4QA6, 4QA7

  • PubMed Abstract: 

    Cornelia de Lange Syndrome (CdLS) is a multiple congenital anomaly disorder resulting from mutations in genes that encode the core components of the cohesin complex, SMC1A, SMC3, and RAD21, or two of its regulatory proteins, NIPBL and HDAC8. HDAC8 is the human SMC3 lysine deacetylase required for cohesin recycling in the cell cycle. To date, 16 different missense mutations in HDAC8 have recently been identified in children diagnosed with CdLS. To understand the molecular effects of these mutations in causing CdLS and overlapping phenotypes, we have fully characterized the structure and function of five HDAC8 mutants: C153F, A188T, I243N, T311M, and H334R. X-ray crystal structures reveal that each mutation causes local structural changes that compromise catalysis and/or thermostability. For example, the C153F mutation triggers conformational changes that block acetate product release channels, resulting in only 2% residual catalytic activity. In contrast, the H334R mutation causes structural changes in a polypeptide loop distant from the active site and results in 91% residual activity, but the thermostability of this mutant is significantly compromised. Strikingly, the catalytic activity of these mutants can be partially or fully rescued in vitro by the HDAC8 activator N-(phenylcarbamothioyl)benzamide. These results suggest that HDAC8 activators might be useful leads in the search for new therapeutic strategies in managing CdLS.


  • Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323 United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 8
A, B
389Homo sapiensMutation(s): 1 
Gene Names: HDAC8HDACL1CDA07
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
PHAROS:  Q9BY41
GTEx:  ENSG00000147099 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY41
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SHH
Query on SHH

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
C14 H20 N2 O3
WAEXFXRVDQXREF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SHH BindingDB:  4QA2 Ki: min: 173, max: 1.57e+4 (nM) from 9 assay(s)
Kd: min: 580, max: 6800 (nM) from 4 assay(s)
IC50: min: 1, max: 1.00e+4 (nM) from 179 assay(s)
EC50: min: 180, max: 1680 (nM) from 4 assay(s)
-TΔS: min: 0.22, max: 10.14 (kJ/mol) from 2 assay(s)
ΔH: min: -4.56e+1, max: -3.75e+1 (kJ/mol) from 2 assay(s)
ΔG: -3.50e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.017α = 90
b = 84.057β = 98.6
c = 94.381γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description