Chromodomain: The chromodomain is the smallest member, consisting of four curved β-strands and an α-helix. The chromodomains of HP1 and Polycomb were found to recognize histone H3 trimethylated at K9 (H3K9me3) and H3K27me3, respectively, and these proteins were the first examples of readers specific for methyllysine. Chromodomains generally prefer trimethylated lysine, though some have been shown to bind dimethylated species. The aromatic cage of the chromodomain of mouse and fly HP1 contains an aspartate or glutamate residue, accounting for its ability to interact well with H3K9me3 and dimethylated H3K9 (H3K9me2). (1)
Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.
DCD: In the double chromodomain (DCD), both chromodomains share their general secondary structure elements with those previously seen in HP1 and Polycomb chromodomains. The linker segment forms a novel helix–turn–helix structure that juxtaposes the two chromodomains to form a continuous surface. A total of 350 Å is buried at the interface of these tandem chromodomains. (1)
Reference
1. John F. Flanagan, Li-Zhi Mi, Maksymilian Chruszcz, Marcin Cymborowski, Katrina L. Clines, Youngchang Kim, Wladek Minor, Fraydoon Rastinejad & Sepideh Khorasanizadeh.Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature.2005;438:1181–1185. PMID: 16372014.
MBT: MBT reads lower methylation states, recognizing mono- and dimethylated lysines. All MBTs characterized at present contain two to four repeats of ~100 amino acids. The most common three-repeat 3MBT module folds in a propeller-like structure, and the four-repeat 4MBT module has an asymmetric rhombus architecture29-32. Notably, although each MBT repeat contains an aromatic cage, which also includes an acidic residue, only the second repeat binds methyllysine. (1)
Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.