3C10

Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with Trichostatin A (TSA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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 %)
TSNKi:  195   nM  BindingDB
TSNIC50:  7.5   nM  BindingDB
TSNIC50:  139   nM  BindingDB
TSNIC50:  2300   nM  BindingDB
TSNIC50:  300   nM  Binding MOAD
TSNIC50:  3.4000000953674316   nM  BindingDB
TSNIC50:  4.599999904632568   nM  BindingDB
TSNIC50:  100   nM  BindingDB
TSNIC50:  1.399999976158142   nM  BindingDB
TSNIC50:  15   nM  BindingDB
TSNIC50:  4290   nM  BindingDB
TSNIC50:  2950   nM  BindingDB
TSNIC50:  197   nM  BindingDB
TSNIC50:  200   nM  BindingDB
TSNIC50:  663   nM  BindingDB
TSNIC50:  26   nM  BindingDB
TSNIC50:  29   nM  BindingDB
TSNIC50:  22   nM  BindingDB
TSNIC50:  23   nM  BindingDB
TSNKi:  504   nM  BindingDB
TSNIC50:  5   nM  BindingDB
TSNIC50:  53   nM  BindingDB
TSNIC50:  55   nM  BindingDB
TSNIC50 :  300   nM  PDBBind
TSNIC50:  3   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.827α = 90
b = 81.827β = 90
c = 148.97γ = 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