Fig. 3.

AGD12, AGD34, and AGD56 of AGDP1 recognize methylated H3K9 by the same mechanism. a A superimposition of the structures of RsAGDP1 AGD12-H3K9me2 complex (in color) and AtAGDP1 AGD34 (in silver) indicate that the AGD12 and AGD34 adopt almost identical overall structures. The H3K4- and H3K9me2-binding residues are highlighted in sticks and they are conserved and occupy the same positions. b A structure-based sequence alignment of AtAGDP1 AGD12, AGD34, and AGD56, and RsAGDP1 AGD12, AGD34, and AGD56 with the secondary structures of RsAGDP1 AGD12 and AtAGDP1 AGD34 highlighted on the top and bottom of the alignment, respectively. The H3K4- and H3K9me2-binding residues are highlighted by stars, and most of them are conserved. We therefore conclude that all the tandem AGD cassettes of AtAGDP1 and RsAGDP1 recognize H3K9me2 via a shared mechanism with conserved peptide-interacting residues. c-f The comparison of the methyllysine-aromatic cage interaction of MPP8 (c, PDB code: 3R93), UHRF1 (d, PDB code: 4GY5), AGDP1 (e), and ORC1 (f, PDB code: 4DOW). The residues are shown in stick representation with the reader and methyllysine residues colored in green and yellow, respectively. The hydrogen bonds between dimethyllysine and the negatively charged residues are highlighted in dashed silver lines