3DB3

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

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
  • Primary Citation of Related Structures:  
    2L3R, 3DB3, 3DB4

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1A161Homo sapiensMutation(s): 0 
Gene Names: UHRF1ICBP90NP95RNF106
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q96T88 (Homo sapiens)
Explore Q96T88 
Go to UniProtKB:  Q96T88
NIH Common Fund Data Resources
PHAROS  Q96T88
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Trimethylated histone H3-K9 peptideB6N/AMutation(s): 0 
Find proteins for Q71DI3 (Homo sapiens)
Explore Q71DI3 
Go to UniProtKB:  Q71DI3
NIH Common Fund Data Resources
PHAROS  Q71DI3
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
M3L
Query on M3L
BL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.622α = 90
b = 99.622β = 90
c = 41.232γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing

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