4QXH

Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


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Literature

A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36.

Cheng, Z., Cheung, P., Kuo, A.J., Yukl, E.T., Wilmot, C.M., Gozani, O., Patel, D.J.

(2014) Genes Dev 28: 1758-1771

  • DOI: 10.1101/gad.246561.114
  • Primary Citation of Related Structures:  
    4QWN, 4QX7, 4QX8, 4QXB, 4QXC, 4QXH, 4TN7

  • PubMed Abstract: 

    • The dynamic reversible methylation of lysine residues on histone proteins is central to chromatin biology. Key components are demethylase enzymes, which remove methyl moieties from lysine residues. KDM2A, a member of the Jumonji C domain-containing histone lysine demethylase family, specifically targets lower methylation states of H3K36 ...

    The dynamic reversible methylation of lysine residues on histone proteins is central to chromatin biology. Key components are demethylase enzymes, which remove methyl moieties from lysine residues. KDM2A, a member of the Jumonji C domain-containing histone lysine demethylase family, specifically targets lower methylation states of H3K36. Here, structural studies reveal that H3K36 specificity for KDM2A is mediated by the U-shaped threading of the H3K36 peptide through a catalytic groove within KDM2A. The side chain of methylated K36 inserts into the catalytic pocket occupied by Ni(2+) and cofactor, where it is positioned and oriented for demethylation. Key residues contributing to K36me specificity on histone H3 are G33 and G34 (positioned within a narrow channel), P38 (a turn residue), and Y41 (inserts into its own pocket). Given that KDM2A was found to also bind the H3K36me3 peptide, we postulate that steric constraints could prevent α-ketoglutarate from undergoing an "off-line"-to-"in-line" transition necessary for the demethylation reaction. Furthermore, structure-guided substitutions of residues in the KDM2A catalytic pocket abrogate KDM2A-mediated functions important for suppression of cancer cell phenotypes. Together, our results deduce insights into the molecular basis underlying KDM2A regulation of the biologically important methylated H3K36 mark.

    Organizational Affiliation: 

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; pateld@mskcc.org ogozani@stanford.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 2AA, C329Mus musculusMutation(s): 0 
Gene Names: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004, Fbl11
EC: 1.14.11.27
UniProt
Find proteins for P59997 (Mus musculus)
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Go to UniProtKB:  P59997
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UniProt GroupP59997
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 2AB, D68Mus musculusMutation(s): 0 
Gene Names: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004, Fbl11
EC: 1.14.11.27
UniProt
Find proteins for P59997 (Mus musculus)
Explore P59997 
Go to UniProtKB:  P59997
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UniProt GroupP59997
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2E, F15Mus musculusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P84228 (Mus musculus)
Explore P84228 
Go to UniProtKB:  P84228
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UniProt GroupP84228
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA
Download Ideal Coordinates CCD File 
G [auth A],
I [auth C]		N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N		 Ligand Interaction
NI
Query on NI
Download Ideal Coordinates CCD File 
H [auth A],
J [auth C]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ		E, F L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
OGA BindingDB:  4QXH IC50: min: 4.50e+4, max: 5.01e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.594α = 90
b = 86.761β = 90
c = 171.073γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release