3Q0B

Crystal structure of SUVH5 SRA- fully methylated CG DNA complex in space group P42212

Summary for 3Q0B

• Entry DOI: 10.2210/pdb3q0b/pdb
• Related: 3Q0C 3Q0D 3Q0F
• Descriptor: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5, DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*T)-3') (3 entities in total)
• Functional Keywords: sra, fully methylated cg, suvh5, 5mc binding protein, fully methylated cg duplex dna, transferase-dna complex, transferase/dna
• Biological source: Arabidopsis thaliana (mouse-ear cress,thale-cress); More
• Cellular location: Nucleus (By similarity): O82175
• Total number of polymer chains: 2
• Total formula weight: 21667.75

Authors

Eerappa, R.,Simanshu, D.K.,Patel, D.J. (deposition date: 2010-12-15, release date: 2011-02-02, Last modification date: 2011-07-13)

Primary citation

Rajakumara, E.,Law, J.A.,Simanshu, D.K.,Voigt, P.,Johnson, L.M.,Reinberg, D.,Patel, D.J.,Jacobsen, S.E.
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.
Genes Dev., 25:137-152, 2011

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 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.

PubMed: 21245167
DOI: 10.1101/gad.1980311

Experimental method

X-RAY DIFFRACTION (2.2 Å)