3DB4

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.

Nady, N.Lemak, A.Walker, J.R.Avvakumov, G.V.Kareta, M.S.Achour, M.Xue, S.Duan, S.Allali-Hassani, A.Zuo, X.Wang, Y.X.Bronner, C.Chedin, F.Arrowsmith, C.H.Dhe-Paganon, S.

(2011) J Biol Chem 286: 24300-24311

  • DOI: 10.1074/jbc.M111.234104
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Histone modifications and DNA methylation represent two layers of heritable epigenetic information that regulate eukaryotic chromatin structure and gene activity. UHRF1 is a unique factor that bridges these two layers; it is required for maintenance ...

    Histone modifications and DNA methylation represent two layers of heritable epigenetic information that regulate eukaryotic chromatin structure and gene activity. UHRF1 is a unique factor that bridges these two layers; it is required for maintenance DNA methylation at hemimethylated CpG sites, which are specifically recognized through its SRA domain and also interacts with histone H3 trimethylated on lysine 9 (H3K9me3) in an unspecified manner. Here we show that UHRF1 contains a tandem Tudor domain (TTD) that recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). Solution NMR and crystallographic data reveal the TTD simultaneously recognizes H3K9me3 through a conserved aromatic cage in the first Tudor subdomain and unmodified H3K4 within a groove between the tandem subdomains. The subdomains undergo a conformational adjustment upon peptide binding, distinct from previously reported mechanisms for dual histone mark recognition. Mutant UHRF1 protein deficient for H3K4me0/K9me3 binding shows altered localization to heterochromatic chromocenters and fails to reduce expression of a target gene, p16(INK4A), when overexpressed. Our results demonstrate a novel recognition mechanism for the combinatorial readout of histone modification states associated with gene silencing and add to the growing evidence for coordination of, and cross-talk between, the modification states of H3K4 and H3K9 in regulation of gene expression.


    Organizational Affiliation

    Ontario Cancer Institute, and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase UHRF1
A
161Homo sapiensMutation(s): 0 
Gene Names: UHRF1ICBP90NP95RNF106
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q96T88 (Homo sapiens)
Go to UniProtKB:  Q96T88
NIH Common Fund Data Resources
PHAROS  Q96T88
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.654α = 90
b = 98.654β = 90
c = 43.345γ = 120
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-18
    Changes: Database references