4EZH

the crystal structure of KDM6B bound with H3K27me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.

Kruidenier, L.Chung, C.W.Cheng, Z.Liddle, J.Che, K.Joberty, G.Bantscheff, M.Bountra, C.Bridges, A.Diallo, H.Eberhard, D.Hutchinson, S.Jones, E.Katso, R.Leveridge, M.Mander, P.K.Mosley, J.Ramirez-Molina, C.Rowland, P.Schofield, C.J.Sheppard, R.J.Smith, J.E.Swales, C.Tanner, R.Thomas, P.Tumber, A.Drewes, G.Oppermann, U.Patel, D.J.Lee, K.Wilson, D.M.

(2012) Nature 488: 404-408

  • DOI: 10.1038/nature11262
  • Primary Citation of Related Structures:  
    4EZH, 4EZ4, 4EYU, 2XUE, 4ASK

  • PubMed Abstract: 
  • The jumonji (JMJ) family of histone demethylases are Fe2+- and α-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes. These enzymes demethylate lysine residues in histones in a methylatio ...

    The jumonji (JMJ) family of histone demethylases are Fe2+- and α-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance, as well as in development, physiology and disease. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX). The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.


    Organizational Affiliation

    Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Stevenage SG1 2NY, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 6BAB486Mus musculusMutation(s): 0 
Gene Names: Kdm6bJmjd3Kiaa0346
EC: 1.14.11 (PDB Primary Data), 1.14.11.68 (UniProt)
Find proteins for Q5NCY0 (Mus musculus)
Explore Q5NCY0 
Go to UniProtKB:  Q5NCY0
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SYNTHESIZED methylation peptideCD11synthetic constructMutation(s): 0 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C,DL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.682α = 90
b = 102.413β = 90
c = 143.2γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-08-15
    Changes: Database references
  • Version 1.2: 2012-08-29
    Changes: Database references
  • Version 1.3: 2017-08-09
    Changes: Refinement description, Source and taxonomy