3Q0D

Crystal structure of SUVH5 SRA- hemi methylated CG DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3704 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo.

Rajakumara, E.Law, J.A.Simanshu, D.K.Voigt, P.Johnson, L.M.Reinberg, D.Patel, D.J.Jacobsen, S.E.

(2011) Genes Dev. 25: 137-152

  • DOI: 10.1101/gad.1980311
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytosine DNA methylation is evolutionarily ancient, and in eukaryotes this epigenetic modification is associated with gene silencing. Proteins with SRA (SET- or RING-associated) methyl-binding domains are required for the establishment and/or mainten ...

    Cytosine DNA methylation is evolutionarily ancient, and in eukaryotes this epigenetic modification is associated with gene silencing. Proteins with SRA (SET- or RING-associated) methyl-binding domains are required for the establishment and/or maintenance of DNA methylation in both plants and mammals. The 5-methyl-cytosine (5mC)-binding specificity of several SRA domains have been characterized, and each one has a preference for DNA methylation in different sequence contexts. Here we demonstrate through mobility shift assays and calorimetric measurements that the SU(VAR)3-9 HOMOLOG 5 (SUVH5) SRA domain differs from other SRA domains in that it can bind methylated DNA in all contexts to similar extents. Crystal structures of the SUVH5 SRA domain bound to 5mC-containing DNA in either the fully or hemimethylated CG context or the methylated CHH context revealed a dual flip-out mechanism where both the 5mC and a base (5mC, C, or G, respectively) from the partner strand are simultaneously extruded from the DNA duplex and positioned within binding pockets of individual SRA domains. Our structure-based in vivo studies suggest that a functional SUVH5 SRA domain is required for both DNA methylation and accumulation of the H3K9 dimethyl modification in vivo, suggesting a role for the SRA domain in recruitment of SUVH5 to genomic loci.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
X, A
167Arabidopsis thalianaMutation(s): 0 
Gene Names: SUVH5 (SDG9, SET9)
EC: 2.1.1.43
Find proteins for O82175 (Arabidopsis thaliana)
Go to UniProtKB:  O82175
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*CP*AP*(5CM)P*GP*TP*CP*AP*G)-3')B10N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*GP*A)-3')C10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
B
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3704 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 76.379α = 90.00
b = 76.379β = 90.00
c = 74.254γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-02-27
    Type: Advisory
  • Version 1.3: 2017-11-08
    Type: Refinement description