2P5B

The complex structure of JMJD2A and trimethylated H3K36 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of the recognition of a methylated histone tail by JMJD2A.

Chen, Z.Zang, J.Kappler, J.Hong, X.Crawford, F.Wang, Q.Lan, F.Jiang, C.Whetstine, J.Dai, S.Hansen, K.Shi, Y.Zhang, G.

(2007) Proc.Natl.Acad.Sci.USA 104: 10818-10823

  • DOI: 10.1073/pnas.0704525104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Jumonji C domain is a catalytic motif that mediates histone lysine demethylation. The Jumonji C-containing oxygenase JMJD2A specifically demethylates tri- and dimethylated lysine-9 and lysine-36 of histone 3 (H3K9/36 me3/2). Here we present struc ...

    The Jumonji C domain is a catalytic motif that mediates histone lysine demethylation. The Jumonji C-containing oxygenase JMJD2A specifically demethylates tri- and dimethylated lysine-9 and lysine-36 of histone 3 (H3K9/36 me3/2). Here we present structures of the JMJD2A catalytic core complexed with methylated H3K36 peptide substrates in the presence of Fe(II) and N-oxalylglycine. We found that the interaction between JMJD2A and peptides largely involves the main chains of the enzyme and the peptide. The peptide-binding specificity is primarily determined by the primary structure of the peptide, which explains the specificity of JMJD2A for methylated H3K9 and H3K36 instead of other methylated residues such as H3K27. The specificity for a particular methyl group, however, is affected by multiple factors, such as space and the electrostatic environment in the catalytic center of the enzyme. These results provide insights into the mechanisms and specificity of histone demethylation.


    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
JmjC domain-containing histone demethylation protein 3A
A, B
352Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
I, J
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

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Download CCD File 
A, B
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
I, J
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.915α = 90.00
b = 150.844β = 90.00
c = 57.346γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-11-27
    Type: Non-polymer description