Chromodomain

The chromodomain is colored red. It is a barrel-like all-beta strand domain, with 2 helices. It is shown bound to residues 2-17 of Histone 3, in which Lys 9 is tri-methylated (colored yellow). The methylated lysine lies on the surface of the chromodomain protein, at one end of the barrel. The long helix lies at the other end of the barrel.

High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin.
Schalch T, Job G, Noffsinger VJ, Shanker S, Kuscu C, Joshua-Tor L, Partridge JF.
Mol Cell. 2009 Apr 10;34(1):36-46.

(PubMed)

3jvk (PDB)

Mind the methyl: methyllysine binding proteins in epigenetic regulation.
Wagner T, Robaa D, Sippl W, Jung M.
ChemMedChem. 2014 Mar;9(3):466-83. doi: 10.1002/cmdc.201300422. Epub 2014 Jan 21. Review.

Abstract
Epigenetics is defined as the phenomenon of heritable phenotypic traits that are not governed by alteration of the genetic code. Major epigenetic control mechanisms include DNA methylation and post-translational modifications of histones, such as reversible histone acetylation and methylation of lysine residues. Methyllysine binding proteins recognize various levels of lysine methylation and mediate the signaling events that are induced by histone methylation. Therefore, they are also referred to as readers of the epigenetic code. In this article we review the current literature on the structure and biology of methyllysine binding proteins, especially with regard to their potential as drug targets. We also present the available inhibitors that block the interaction of methylated histones with their binding proteins.

Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription.
Yap KL, Zhou MM.
Biochemistry. 2011 Mar 29;50(12):1966-80. doi: 10.1021/bi101885m. Epub 2011 Feb 23. Review.
PMC

Abstract
Histone methylation recognition is accomplished by a number of evolutionarily conserved protein domains, including those belonging to the methylated lysine-binding Royal family of structural folds. One well-known member of the Royal family, the chromodomain, is found in the HP1/chromobox and CHD subfamilies of proteins, in addition to a small number of other proteins that are involved in chromatin remodeling and gene transcriptional silencing. Here we discuss the structure and function of the chromodomain within these proteins as methylated histone lysine binders and how the functions of these chromodomains can be modulated by additional post-translational modifications or binding to nucleic acids.