Bromodomain: Bromodomains (BRDs) are protein interaction modules that exclusively recognize acetylation motifs. BRDs are evolutionarily conserved and present in diverse nuclear proteins comprising HATs (GCN5, PCAF), ATP-dependent chromatin-remodeling complexes (BAZ1B), helicases (SMARCA), methyltransferases (MLL, ASH1L), transcriptional coactivators (TRIM/TIF1, TAFs) transcriptional mediators (TAF1), nuclear-scaffolding proteins(PB1), and the BET family. Despite large sequence variations, all BRD modules share a conserved fold that comprises a left-handed bundle of four a helices, linked by loop regions of variablelength, which line the Kac binding site and determine binding specificity. (1)
Reference
1. P. Filippakopoulos, S. Picaud, M. Mangos, T. Keates, J.P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S. Müller, T. Pawson,et al.Histone recognition and large-scale structural analysis of the human bromodomain family. Cell.2012;149(1):214-231. PMID: 22464331.
Tandem-PHD: Acetylated lysines (AcKs) can be recognized by the tandem PHD domain. Besides, the bromo domain of Brdt has a much wider pocket, which holds two AcKs simultaneously; whereas the tandem PHD has a shallow cage. Many bromo domains bind to multiple acetylated histones and the tandem PHD domain of human DPF3b also prefers acetylated H3 and H4, indicating the lack of unique sequence recognition by these readers. (1)
Reference
1. Yun M, Wu J, Workman JL, Li B.Readers of histone modifications. Cell Res.2011;21:564-578. PMID: 21423274.