3ZLI

Crystal structure of JmjC domain of human histone demethylase UTY

• PDB DOI: https://doi.org/10.2210/pdb3ZLI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-01-31 Released: 2013-02-27 
• Deposition Author(s): Vollmar, M., Gileadi, C., Shrestha, L., Goubin, S., Johansson, C., Krojer, T., Raynor, J.W., Bradley, A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Starting Model: experimental

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

• PubMed: 24798337 
• DOI: https://doi.org/10.1074/jbc.M114.555052
• Primary Citation of Related Structures:  
  3ZLI, 3ZPO


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.42 kDa 
• Atom Count: 7,747 
• Modelled Residue Count: 882 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE DEMETHYLASE UTY	A, B	478	Homo sapiens	Mutation(s): 0  EC: 1.14.11 (PDB Primary Data), 1.14.11.68 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14607 (Homo sapiens) Explore O14607  Go to UniProtKB:  O14607
PHAROS:  O14607 GTEx:  ENSG00000183878

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	K [auth A], T [auth B]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
ZN	M [auth A], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2	L [auth A], U [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.585	α = 90
b = 110.249	β = 90
c = 118.242	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Vollmar, M., Gileadi, C., Shrestha, L., Goubin, S., Johansson, C., Krojer, T., Raynor, J.W., Bradley, A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2014-01-29
  Changes: Atomic model, Derived calculations, Non-polymer description
• Version 1.2: 2015-05-20
  Changes: Database references, Other
• Version 1.3: 2019-10-09
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description