Asked • 07/09/19

What is an aromatic cage and what does it do?

Epigenetics, 2. ed, Chapter 3.6:> Similarly, methylated lysine residues embedded in histone tails can be> read by “aromatic cages” present in chromodomains, or similar domains> (e.g., MBT, Tudor) contained within complexes that facilitate> downstream chromatin modulating events (see Ch. 7 [Patel 2014] for> structural insightsI understand it is something like a protein motif, but I cannot find a good definition using google.

Sorita D.

To different degrees, all aromatic amino acids absorb ultraviolet light. Tyrosine and tryptophan absorb more than do phenylalanine; tryptophan is responsible for most of the absorbance of ultraviolet light (ca. 280 nm) by proteins. Tyrosine is the only one of the aromatic amino acids with an ionizable side chain.For example, Generally, the residues that are used to form the aromatic cage exists in parts of the structure that are rigid, such as β-strand or close to the Zn-coordinating Cys residue. At minimum, two aromatic residues that include the invariable Trp at position 1, appears to be necessary for the H3K4me3 binding. The simplest observed so far aromatic cage is that of jumonji, which is the AT-rich interactive domain 1A (JARID1A), and is composed of only two Trp residues that are at both positions 1 and 2. Together with JARID1A, the aromatic cage of recombination active gene 2 (RAG2) and myeloid/lymphoid or mixed-lineage leukemeia-1 (MLL1) lack the 'lid' residues that are present at position 3 in all other PHD finger aromatic cages.
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08/06/19

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Mithony K. answered • 08/30/20

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We can try to ascertain the definition of an aromatic cage and what it does by breaking it down. An aromatic compound is a ring compound that is resonance stabilized by the delocalization of electrons within the molecule. Therefore, an aromatic cage would be simply an arrangement of several aromatic compounds to form a cage-like molecular complex. Since this aromatic cage is electron rich, it is likely use to stabilize or contain an electron poor entity (molecule, ion, etc.)

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