3C0Z

Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with SAHA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity.

Schuetz, A.Min, J.Allali-Hassani, A.Schapira, M.Shuen, M.Loppnau, P.Mazitschek, R.Kwiatkowski, N.P.Lewis, T.A.Maglathin, R.L.McLean, T.H.Bochkarev, A.Plotnikov, A.N.Vedadi, M.Arrowsmith, C.H.

(2008) J Biol Chem 283: 11355-11363

  • DOI: 10.1074/jbc.M707362200
  • Primary Citation of Related Structures:  
    3C0Y, 3C0Z, 3C10

  • PubMed Abstract: 
  • Histone deacetylases (HDACs) are protein deacetylases that play a role in repression of gene transcription and are emerging targets in cancer therapy. Here, we characterize the structure and enzymatic activity of the catalytic domain of human HDAC7 (cdHD ...

    Histone deacetylases (HDACs) are protein deacetylases that play a role in repression of gene transcription and are emerging targets in cancer therapy. Here, we characterize the structure and enzymatic activity of the catalytic domain of human HDAC7 (cdHDAC7). Although HDAC7 normally exists as part of a multiprotein complex, we show that cdHDAC7 has a low level of deacetylase activity which can be inhibited by known HDAC inhibitors. The crystal structures of human cdHDAC7 and its complexes with two hydroxamate inhibitors are the first structures of the catalytic domain of class IIa HDACs and demonstrate significant differences with previously reported class I and class IIb-like HDAC structures. We show that cdHDAC7 has an additional class IIa HDAC-specific zinc binding motif adjacent to the active site which is likely to participate in substrate recognition and protein-protein interaction and may provide a site for modulation of activity. Furthermore, a different active site topology results in modified catalytic properties and in an enlarged active site pocket. Our studies provide mechanistic insights into class IIa HDACs and facilitate the design of specific modulators.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L5, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 7a ABC423Homo sapiensMutation(s): 0 
Gene Names: HDAC7AHDAC7
EC: 3.5.1.98
Find proteins for Q8WUI4 (Homo sapiens)
Explore Q8WUI4 
Go to UniProtKB:  Q8WUI4
NIH Common Fund Data Resources
PHAROS:  Q8WUI4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SHHKi:  2470   nM  BindingDB
SHHKd:  36000   nM  BindingDB
SHHIC50:  1100   nM  BindingDB
SHHIC50:  2.799999952316284   nM  BindingDB
SHHIC50 :  113000   nM  PDBBind
SHHIC50:  12   nM  BindingDB
SHHIC50:  10   nM  BindingDB
SHHIC50:  2590   nM  BindingDB
SHHIC50:  2480   nM  BindingDB
SHHIC50:  2056   nM  BindingDB
SHHIC50:  6110   nM  BindingDB
SHHIC50:  5044   nM  BindingDB
SHHIC50:  15   nM  BindingDB
SHHIC50:  53   nM  BindingDB
SHHIC50:  1   nM  BindingDB
SHHIC50:  34   nM  BindingDB
SHHIC50:  7200   nM  BindingDB
SHHIC50:  105   nM  BindingDB
SHHIC50:  100   nM  BindingDB
SHHIC50:  102   nM  BindingDB
SHHIC50:  99   nM  BindingDB
SHHIC50:  90   nM  BindingDB
SHHIC50:  80   nM  BindingDB
SHHIC50:  79   nM  BindingDB
SHHIC50:  65   nM  BindingDB
SHHIC50:  67   nM  BindingDB
SHHEC50:  550   nM  BindingDB
SHHIC50:  55   nM  BindingDB
SHHIC50:  200   nM  BindingDB
SHHEC50:  180   nM  BindingDB
SHHIC50:  194   nM  BindingDB
SHHIC50:  196   nM  BindingDB
SHHIC50:  113000   nM  Binding MOAD
SHHIC50:  156   nM  BindingDB
SHHIC50:  145   nM  BindingDB
SHHIC50:  140   nM  BindingDB
SHHIC50:  141   nM  BindingDB
SHHIC50:  130   nM  BindingDB
SHHIC50:  120   nM  BindingDB
SHHIC50:  122   nM  BindingDB
SHHKi:  129   nM  BindingDB
SHHIC50:  110   nM  BindingDB
SHHIC50:  10000   nM  BindingDB
SHHIC50:  344   nM  BindingDB
SHHIC50:  330   nM  BindingDB
SHHIC50:  280   nM  BindingDB
SHHIC50:  260   nM  BindingDB
SHHIC50:  560   nM  BindingDB
SHHIC50:  500   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.825α = 90
b = 81.825β = 90
c = 148.867γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance