3Q0D: Crystal structure of SUVH5 SRA- hemi methylated CG DNA complex

Citation:
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 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.
PDB ID: 3Q0DDownload
MMDB ID: 88855
PDB Deposition Date: 2010/12/15
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.3704  Å
Source Organism:
Arabidopsis thaliana
Similar Structures:
Biological Unit for 3Q0D: tetrameric; determined by author and by software (PISA)
Molecular Components in 3Q0D
Label Count Molecule
Proteins (2 molecules)
2
Histone-lysine N-methyltransferase, H3 Lysine-9 Specific Suvh5(Gene symbol: SUVH5)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*tp*cp*cp*ap*(5cm)p*gp*tp*cp*ap*g)-3')
Molecule annotation
1
DNA (5'-d(*cp*tp*gp*ap*cp*gp*tp*gp*gp*a)-3')
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.