2W2I

Crystal structure of the human 2-oxoglutarate oxygenase LOC390245

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 

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
2-OXOGLUTARATE OXYGENASE
A, B, C
358Homo sapiensMutation(s): 0 
Gene Names: KDM4E (KDM4DL)
EC: 1.14.11.-
Find proteins for B2RXH2 (Homo sapiens)
Go to Gene View: KDM4E
Go to UniProtKB:  B2RXH2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PD2
Query on PD2
Download SDF File 
Download CCD File 
A, B, C
PYRIDINE-2,4-DICARBOXYLIC ACID
C7 H5 N O4
MJIVRKPEXXHNJT-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI
Download SDF File 
Download CCD File 
A, B, C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PD2IC50: 1400 nM (100) BINDINGDB
PD2Ki: 914000 nM (100) BINDINGDB
PD2Ki: 914 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.904α = 90.00
b = 111.009β = 90.00
c = 224.199γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2015-05-13
    Type: Database references, Non-polymer description, Other, Refinement description, Source and taxonomy