2GP5

Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into histone demethylation by JMJD2 family members

Chen, Z.Zang, J.Whetstine, J.Hong, X.Davrazou, F.Kutateladze, T.G.Simpson, M.Mao, Q.Pan, C.H.Dai, S.Hagman, J.Hansen, K.Shi, Y.Zhang, G.

(2006) Cell 125: 691-702

  • DOI: 10.1016/j.cell.2006.04.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Posttranslational modifications of histones regulate chromatin structure and gene expression. Histone demethylases, members of a newly emerging transcription-factor family, remove methyl groups from the lysine residues of the histone tails and thereb ...

    Posttranslational modifications of histones regulate chromatin structure and gene expression. Histone demethylases, members of a newly emerging transcription-factor family, remove methyl groups from the lysine residues of the histone tails and thereby regulate the transcriptional activity of target genes. JmjC-domain-containing proteins have been predicted to be demethylases. For example, the JmjC-containing protein JMJD2A has been characterized as a H3-K9me3- and H3-K36me3-specific demethylase. Here, structures of the catalytic-core domain of JMJD2A with and without alpha-ketoglutarate in the presence of Fe2+ have been determined by X-ray crystallography. The structure of the core domain, consisting of the JmjN domain, the JmjC domain, the C-terminal domain, and a zinc-finger motif, revealed the unique elements that form a potential substrate binding pocket. Sited-directed mutagenesis in conjunction with demethylase activity assays allowed us to propose a molecular model for substrate selection by the JMJD2 histone demethylase family.


    Organizational Affiliation

    Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Jumonji domain-containing protein 2A
A, B
349Homo sapiensMutation(s): 0 
Gene Names: KDM4A (JHDM3A, JMJD2, JMJD2A, KIAA0677)
EC: 1.14.11.-
Find proteins for O75164 (Homo sapiens)
Go to Gene View: KDM4A
Go to UniProtKB:  O75164
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A, B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.107α = 90.00
b = 149.524β = 90.00
c = 57.028γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2013-11-27
    Type: Non-polymer description