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Interactions of Pc monomers in Pc dimer Involvement of carbonyl groups of Leu 20 and Thr 22 of histone H3 in forming of hydrogen bonds with the side chain NH2 groups of Arg 67, is a PC-specific interaction. This interaction would not be possible with the HP1 protein, as Arg 67 is not conserved and is instead substituted by Asp 62 in HP1. The interactions between Arg 67 and Leu 20 and Thr 22 of H3K27me3 cannot be considered for the binding specificity since only the main-chain atoms of histone H3 are involved in the interactions.
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The side chain of Leu 20 is positioned in a hydrophobic pocket formed by the side chains of Val 25 and Ala 27 of another PC molecule in the dimer, and the side chains of Thr 22 and Ala 24 of the other histone H3 peptide. This recognition mode can effectively exclude the binding of a H3K9me3, as the residues corresponding to Leu 20, Thr 22, and Ala 24 of histone H3 would be Arg 2, Lys 4, and Thr 5, respectively. Replacement of Leu 20 and Thr 22 with an arginine and a lysine, respectively, introduce extra steric conflicts and is disfavored from an energetic standpoint. Min J, Zhang Y, and Xu R. 2013. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes & Development. 17(15):1823-8. (PubMed) 1PFB (PDB) |