3ZLI

Crystal structure of JmjC domain of human histone demethylase UTY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human Uty(Kdm6C) is a Male-Specific Nepsilon-Methyl Lysyl Demethylase.

Walport, L.J.Hopkinson, R.J.Vollmar, M.Madden, S.K.Gileadi, C.Oppermann, U.Schofield, C.J.Johansson, C.

(2014) J.Biol.Chem. 289: 18302

  • DOI: 10.1074/jbc.M114.555052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Jumonji C lysine demethylases (KDMs) are 2-oxoglutarate- and Fe(II)-dependent oxygenases. KDM6A (UTX) and KDM6B (JMJD3) are KDM6 subfamily members that catalyze demethylation of N(ϵ)-methylated histone 3 lysine 27 (H3K27), a mark important for tr ...

    The Jumonji C lysine demethylases (KDMs) are 2-oxoglutarate- and Fe(II)-dependent oxygenases. KDM6A (UTX) and KDM6B (JMJD3) are KDM6 subfamily members that catalyze demethylation of N(ϵ)-methylated histone 3 lysine 27 (H3K27), a mark important for transcriptional repression. Despite reports stating that UTY(KDM6C) is inactive as a KDM, we demonstrate by biochemical studies, employing MS and NMR, that UTY(KDM6C) is an active KDM. Crystallographic analyses reveal that the UTY(KDM6C) active site is highly conserved with those of KDM6B and KDM6A. UTY(KDM6C) catalyzes demethylation of H3K27 peptides in vitro, analogously to KDM6B and KDM6A, but with reduced activity, due to point substitutions involved in substrate binding. The results expand the set of human KDMs and will be of use in developing selective KDM inhibitors.


    Organizational Affiliation

    From the Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE DEMETHYLASE UTY
A, B
478Homo sapiensMutation(s): 0 
Gene Names: UTY (KDM6C)
EC: 1.14.11.-
Find proteins for O14607 (Homo sapiens)
Go to Gene View: UTY
Go to UniProtKB:  O14607
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A, B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.585α = 90.00
b = 110.249β = 90.00
c = 118.242γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2014-01-29
    Type: Atomic model, Derived calculations, Non-polymer description
  • Version 1.2: 2015-05-20
    Type: Database references, Other