6H8P

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.983 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.

Walport, L.J.Hopkinson, R.J.Chowdhury, R.Zhang, Y.Bonnici, J.Schiller, R.Kawamura, A.Schofield, C.J.

(2018) FEBS Lett. 592: 3264-3273

  • DOI: 10.1002/1873-3468.13231

  • PubMed Abstract: 
  • N-Methylation of lysyl residues is widely observed on histone proteins. Using isolated enzymes, we report mechanistic and structural studies on histone lysine demethylase (KDM)-catalysed demethylation of N <sup>ε </sup> -methylated lysine 26 on histo ...

    N-Methylation of lysyl residues is widely observed on histone proteins. Using isolated enzymes, we report mechanistic and structural studies on histone lysine demethylase (KDM)-catalysed demethylation of N ε -methylated lysine 26 on histone 1 isotype 4 (H1.4). The results reveal that methylated H1.4K26 is a substrate for all members of the KDM4 subfamily and that KDM4A-catalysed demethylation of H1.4K26me3 peptide is similarly efficient to that of H3K9me3. Crystallographic studies of an H1.4K26me3:KDM4A complex reveal a conserved binding geometry to that of H3K9me3. In the light of the high activity of the KDM4s on this mark, our results suggest JmjC KDM-catalysed demethylation of H1.4K26 may be as prevalent as demethylation on the H3 tail and warrants further investigation in cells.


    Related Citations: 
    • 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


    Organizational Affiliation

    Leicester Institute of Structural and Chemical Biology and Department of Chemistry, University of Leicester, UK.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, UK.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4A
A, B
381Homo 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
Histone H1.4
C, D
15Homo sapiensMutation(s): 0 
Gene Names: H1-4 (H1F4, HIST1H1E)
Find proteins for P10412 (Homo sapiens)
Go to UniProtKB:  P10412
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

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A, B
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.983 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.722α = 90.00
b = 150.146β = 90.00
c = 57.601γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references