4QX8

Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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 h ...

    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.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Biology, Stanford University, Stanford, California 94305, USA;,Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA;,Department of Biology, Stanford University, Stanford, California 94305, USA; pateld@mskcc.org ogozani@stanford.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 2A
A, C
329Mus musculusMutation(s): 0 
Gene Names: Kdm2a (Fbxl11, Jhdm1a, Kiaa1004)
EC: 1.14.11.27
Find proteins for P59997 (Mus musculus)
Go to UniProtKB:  P59997
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 2A
B, D
68Mus musculusMutation(s): 0 
Gene Names: Kdm2a (Fbxl11, Jhdm1a, Kiaa1004)
EC: 1.14.11.27
Find proteins for P59997 (Mus musculus)
Go to UniProtKB:  P59997
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
E, F
15Mus musculusMutation(s): 0 
Gene Names: Hist1h3b, Hist1h3c, Hist1h3d, Hist1h3e, Hist1h3f, Hist2h3b, Hist2h3c1, Hist2h3c2 (H3-53, H3.2, H3b, H3-143, H3-B, H3-F, H3.2-221, H3f, H3.2-616, H3.2-615, Hist2h3ca1, H3.2-614, Hist2h3ca2)
Find proteins for P84228 (Mus musculus)
Go to UniProtKB:  P84228
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

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

Download SDF File 
Download CCD File 
A, C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
E, F
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.797α = 90.00
b = 84.615β = 90.00
c = 170.077γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary