4FSX

crystal structure of Se-substituted Zea mays ZMET2 in complex with SAH

Summary for 4FSX

• Entry DOI: 10.2210/pdb4fsx/pdb
• Related: 4FT2 4FT4
• Descriptor: DNA (cytosine-5)-methyltransferase 1, S-ADENOSYL-L-HOMOCYSTEINE (2 entities in total)
• Functional Keywords: chromodomain, bah domain, dna methyltransferase domain, h3k9me2 binding, transferase
• Biological source: Zea mays (maize)
• Cellular location: Nucleus (By similarity): Q9AXT8
• Total number of polymer chains: 2
• Total formula weight: 177453.17

Authors

Du, J.,Patel, D.J. (deposition date: 2012-06-27, release date: 2012-10-17)

Primary citation

Du, J.,Zhong, X.,Bernatavichute, Y.V.,Stroud, H.,Feng, S.,Caro, E.,Vashisht, A.A.,Terragni, J.,Chin, H.G.,Tu, A.,Hetzel, J.,Wohlschlegel, J.A.,Pradhan, S.,Patel, D.J.,Jacobsen, S.E.
Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants.
Cell(Cambridge,Mass.), 151:167-180, 2012

PubMed Abstract: DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification.

PubMed: 23021223
DOI: 10.1016/j.cell.2012.07.034

Experimental method

X-RAY DIFFRACTION (3.2 Å)