1TQE

Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of Recruitment of Class II Histone Deacetylases by Myocyte Enhancer Factor-2.

Han, A.He, J.Wu, Y.Liu, J.O.Chen, L.

(2005) J Mol Biol 345: 91-102

  • DOI: 10.1016/j.jmb.2004.10.033
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Class II histone deacetylases (HDACs) bind myocyte enhancer factor-2 (MEF2) and repress specific gene expression in a calcium-dependent manner. Despite their significant physiological functions in muscle, immune and neuronal cells, the mechanism of r ...

    Class II histone deacetylases (HDACs) bind myocyte enhancer factor-2 (MEF2) and repress specific gene expression in a calcium-dependent manner. Despite their significant physiological functions in muscle, immune and neuronal cells, the mechanism of recruitment of class II HDACs by MEF2 is not well understood. Here, we have characterized the complex between the MEF2-binding motif of class II HDACs and the MADS-box/MEF2S domain of MEF2B by structural and biochemical methods. The crystal structure of a HDAC9/MEF2/DNA complex reveals that HDAC9 binds to a hydrophobic groove of the MEF2 dimer. The overall binding mode is similar to that seen in the Cabin1/MEF2/DNA complex. The detailed binding interactions at the HDAC9/MEF2 interface, however, show marked differences from those at the Cabin1/MEF2 interface. Our studies suggest a general mechanism by which class II HDACs and possibly other transcriptional co-regulators are recruited by MEF2. On the other hand, the differential binding between MEF2 and its various partners may confer specific regulatory and functional properties to MEF2 in distinct cellular processes. Such specificity provides a basis for selectively disrupting a particular MEF2/co-regulator complex by mutations or small molecules.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Myocyte-specific enhancer factor 2BP, Q, R, S93Homo sapiensMutation(s): 0 
Gene Names: MEF2BXMEF2
Find proteins for Q02080 (Homo sapiens)
Explore Q02080 
Go to UniProtKB:  Q02080
NIH Common Fund Data Resources
PHAROS  Q02080
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 9X, Y26Mus musculusMutation(s): 0 
Gene Names: Hdac9Hdac7bHdrpMitr
EC: 3.5.1.98
Find proteins for Q99N13 (Mus musculus)
Explore Q99N13 
Go to UniProtKB:  Q99N13
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganism
MEF2 binding site of nur77 promoterD, F17N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
MEF2 binding site of nur77 promoterC, E17N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.263 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.797α = 76.67
b = 66.93β = 71.83
c = 66.967γ = 71.81
Software Package:
Software NamePurpose
CrystalCleardata collection
SCALEPACKdata scaling
CNSrefinement
CrystalCleardata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description