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 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 

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:  

  • 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 ( ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 7a
A, B, C
423Homo sapiensMutation(s): 0 
Gene Names: HDAC7 (HDAC7A)
EC: 3.5.1.98
Find proteins for Q8WUI4 (Homo sapiens)
Go to Gene View: HDAC7
Go to UniProtKB:  Q8WUI4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
TSN
Query on TSN

Download SDF File 
Download CCD File 
A, B, C
TRICHOSTATIN A
7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE
C17 H22 N2 O3
RTKIYFITIVXBLE-QEQCGCAPSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TSNIC50: 7.5 - 2950 nM (100) BINDINGDB
TSNKi: 195 nM (100) BINDINGDB
TSNIC50: 300 nM BINDINGMOAD
TSNIC50: 300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 81.827α = 90.00
b = 81.827β = 90.00
c = 148.970γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
ARP/wARPmodel building
REFMACrefinement
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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