3AVR

Catalytic fragment of UTX/KDM6A bound with histone H3K27me3 peptide, N-oxyalylglycine, and Ni(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.803 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A

Sengoku, T.Yokoyama, S.

(2011) Genes Dev. 25: 2266-2277

  • DOI: 10.1101/gad.172296.111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tri- and dimethylations of histone H3K9 (H3K9me3/2) and H3K27 (H3K27me3/2), both situated in the "A-R-Kme-S" sequence motif, mediate transcriptional repression of distinct genomic regions. H3K9me3/2 mainly governs constitutive heterochromatin formati ...

    Tri- and dimethylations of histone H3K9 (H3K9me3/2) and H3K27 (H3K27me3/2), both situated in the "A-R-Kme-S" sequence motif, mediate transcriptional repression of distinct genomic regions. H3K9me3/2 mainly governs constitutive heterochromatin formation, while H3K27me3/2 represses key developmental genes. The mechanisms by which histone-modifying enzymes selectively regulate the methylation states of H3K9 and H3K27 are poorly understood. Here we report the crystal structures of the catalytic fragment of UTX/KDM6A, an H3K27me3/2-specific demethylase, in the free and H3 peptide-bound forms. The catalytic jumonji domain binds H3 residues 25-33, recognizing H3R26, H3A29, and H3P30 in a sequence-specific manner, in addition to H3K27me3 in the catalytic pocket. A novel zinc-binding domain, conserved within the KDM6 family, binds residues 17-21 of H3. The zinc-binding domain changes its conformation upon H3 binding, and thereby recognizes the H3L20 side chain via a hydrophobic patch on its surface, which is inaccessible in the H3-free form. Mutational analyses showed that H3R17, H3L20, H3R26, H3A29, H3P30, and H3T32 are each important for demethylation. No other methyllysines in the histone tails have the same set of residues at the corresponding positions. Thus, we clarified how UTX discriminates H3K27me3/2 from the other methyllysines with distinct roles, including the near-cognate H3K9me3/2, in histones.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 6A
A
531Homo sapiensMutation(s): 0 
Gene Names: KDM6A (UTX)
EC: 1.14.11.-
Find proteins for O15550 (Homo sapiens)
Go to Gene View: KDM6A
Go to UniProtKB:  O15550
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
B
22Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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

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Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.803 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.905α = 90.00
b = 83.081β = 90.00
c = 95.057γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-12-14
    Type: Database references