4TN7

Crystal structure of mouse KDM2A-H3K36ME-NO complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 

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 (Fbl11, 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 (Fbl11, Fbxl11, Jhdm1a, Kiaa1004)
EC: 1.14.11.27
Find proteins for P59997 (Mus musculus)
Go to UniProtKB:  P59997
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide
E, F
15Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download SDF File 
Download CCD File 
A, C
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
NO
Query on NO

Download SDF File 
Download CCD File 
A
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
E, F
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.063α = 90.00
b = 157.928β = 90.00
c = 48.706γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-06-03 
  • Released Date: 2015-05-13 
  • Deposition Author(s): Cheng, Z.

Funding OrganizationLocationGrant Number
Lymphoma Society and the STARR foundationUnited States--
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM079641
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM066569
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32 GM097779

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Source and taxonomy, Structure summary