Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.98 kDa 
• Atom Count: 6287 
• Modelled Residue Count: 713 
• Deposited Residue Count: 778 
• Unique protein chains: 2

2OX0

Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9

• DOI: 10.2210/pdb2OX0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-19 Released: 2007-03-13 
• Deposition Author(s): Pilka, E.S., Ng, S.S., Kavanagh, K.L., McDonough, M.A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.

Ng, S.S., Kavanagh, K.L., McDonough, M.A., Butler, D., Pilka, E.S., Lienard, B.M., Bray, J.E., Savitsky, P., Gileadi, O., von Delft, F., Rose, N.R., Offer, J., Scheinost, J.C., Borowski, T., Sundstrom, M., Schofield, C.J., Oppermann, U.

(2007) Nature 448: 87-91

• PubMed: 17589501 
• DOI: 10.1038/nature05971
• Primary Citation of Related Structures:  
  2OT7, 2OX0, 2OQ7, 2OQ6, 2OS2


• PubMed Abstract: 
  

Post-translational histone modification has a fundamental role in chromatin biology and is proposed to constitute a 'histone code' in epigenetic regulation. Differential methylation of histone H3 and H4 lysyl residues regulates processes including heterochromatin formation, X-chromosome inactivation, genome imprinting, DNA repair and transcriptional regulation. The discovery of lysyl demethylases using flavin (amine oxidases) or Fe(II) and 2-oxoglutarate as cofactors (2OG oxygenases) has changed the view of methylation as a stable epigenetic marker. However, little is known about how the demethylases are selective for particular lysyl-containing sequences in specific methylation states, a key to understanding their functions. Here we reveal how human JMJD2A (jumonji domain containing 2A), which is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), discriminates between methylation states and achieves sequence selectivity for H3K9. We report structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. We propose a mechanism for achieving methylation state selectivity involving the orientation of the substrate methyl groups towards a ferryl intermediate. The results suggest distinct recognition mechanisms in different demethylase subfamilies and provide a starting point to develop chemical tools for drug discovery and to study and dissect the complexity of reversible histone methylation and its role in chromatin biology.

---

Organizational Affiliation: 

Structural Genomics Consortium, Botnar Research Center, University of Oxford, Oxford OX3 7LD, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JmjC domain-containing histone demethylation protein 3A	A, B	381	Homo sapiens	Mutation(s): 0  Gene Names: JMJD2A, JHDM3A, JMJD2, KIAA0677, KDM4A EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
Find proteins for O75164 (Homo sapiens) Explore O75164  Go to UniProtKB:  O75164
NIH Common Fund Data Resources
PHAROS:  O75164 GTEx:  ENSG00000066135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
synthetic peptide	C, D	8	N/A	Mutation(s): 0
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS:  P68431 GTEx:  ENSG00000197409ENSG00000197153ENSG00000278828ENSG00000275714ENSG00000273983ENSG00000274750ENSG00000275379ENSG00000277775

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA	H [auth A], K [auth B]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
ZN	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	E [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	C, D	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS
MLY	C, D	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
OGA	IC50:  250000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.21	α = 90
b = 150.004	β = 90
c = 57.228	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-19 
• Released Date: 2007-03-13 
Deposition Author(s): Pilka, E.S., Ng, S.S., Kavanagh, K.L., McDonough, M.A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2007-10-15
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance