2XML

Crystal structure of human JMJD2C catalytic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Evolutionary Basis for the Dual Substrate Selectivity of Human Kdm4 Histone Demethylase Family.

Hillringhaus, L.Yue, W.W.Rose, N.R.Ng, S.S.Gileadi, C.Loenarz, C.Bello, S.H.Bray, J.E.Schofield, C.J.Oppermann, U.

(2011) J.Biol.Chem. 286: 41616

  • DOI: 10.1074/jbc.M111.283689
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N(ε)-Methylations of histone lysine residues play critical roles in cell biology by "marking" chromatin for transcriptional activation or repression. Lysine demethylases reverse N(ε)-methylation in a sequence- and methylation-selective manner. The de ...

    N(ε)-Methylations of histone lysine residues play critical roles in cell biology by "marking" chromatin for transcriptional activation or repression. Lysine demethylases reverse N(ε)-methylation in a sequence- and methylation-selective manner. The determinants of sequence selectivity for histone demethylases have been unclear. The human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone. Kinetic, crystallographic, and mutagenetic studies in vitro and in cells on KDM4A-E reveal that selectivity is determined by multiple interactions within the catalytic domain but outside the active site. Structurally informed phylogenetic analyses reveal that KDM4A-C orthologues exist in all genome-sequenced vertebrates with earlier animals containing only a single KDM4 enzyme. KDM4D orthologues only exist in eutherians (placental mammals) where they are conserved, including proposed substrate sequence-determining residues. The results will be useful for the identification of inhibitors for specific histone demethylases.


    Organizational Affiliation

    Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 4C
A, B
348Homo sapiensMutation(s): 0 
Gene Names: KDM4C (GASC1, JHDM3C, JMJD2C, KIAA0780)
EC: 1.14.11.-
Find proteins for Q9H3R0 (Homo sapiens)
Go to Gene View: KDM4C
Go to UniProtKB:  Q9H3R0
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
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-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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Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OGAIC50: 41500 - 500000 nM (100) BINDINGDB
OGAIC50: 500000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.196 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.660α = 90.00
b = 95.870β = 90.00
c = 100.690γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2012-12-05
    Type: Database references, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2015-05-13
    Type: Database references