2W2I

Crystal structure of the human 2-oxoglutarate oxygenase LOC390245


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    2W2I, 2XML

  • 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 determinants of sequence selectivity for histone demethylases have been unclear ...

    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

    Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom; Botnar Research Centre, National Institute for Health Research Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, Oxford, OX3 7LD, United Kingdom. Electronic address: udo.oppermann@sgc.ox.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-OXOGLUTARATE OXYGENASEA, B, C358Homo sapiensMutation(s): 0 
Gene Names: KDM4EKDM4DL
EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for B2RXH2 (Homo sapiens)
Explore B2RXH2 
Go to UniProtKB:  B2RXH2
PHAROS:  B2RXH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RXH2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PD2 BindingDB:  2W2I Ki: 9.14e+5 (nM) from 1 assay(s)
IC50: min: 1400, max: 6310 (nM) from 2 assay(s)
PDBBind:  2W2I Ki: 914 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.904α = 90
b = 111.009β = 90
c = 224.199γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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