5D6Y

Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.287 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reader domain specificity and lysine demethylase-4 family function.

Su, Z.Wang, F.Lee, J.H.Stephens, K.E.Papazyan, R.Voronina, E.Krautkramer, K.A.Raman, A.Thorpe, J.J.Boersma, M.D.Kuznetsov, V.I.Miller, M.D.Taverna, S.D.Phillips, G.N.Denu, J.M.

(2016) Nat Commun 7: 13387-13387

  • DOI: 10.1038/ncomms13387
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microar ...

    The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.


    Organizational Affiliation

    Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.,Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.,Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA.,Biosciences at Rice, Rice University, Houston, Texas 77005, USA.,Department of Chemistry, Rice University, Houston, Texas 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4A
A, B, C, D, E, F
121Homo 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
peptide H3K23me3 (19-28)
a, b, c, d
10Homo 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
a, b, c, d
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 106.159α = 90.00
b = 106.159β = 90.00
c = 79.206γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU01GM098248
National Institutes of Health/National Institute of General Medical SciencesUnited States2R37GM059785-15/P250VA

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence