The ATPase family, AAA+ domain-containing protein 2B (ATAD2B) is a nuclear protein that may play a role in the development of neuronal tissues and tumorigenesis. The ATAD2B protein contains a C-terminal bromodomain that is highly homologous to the ATAD2 bromodomain, with 74.7% sequence identity and 94.4% similarity. The ATAD2 bromodomain is an attractive drug target because overexpression of ATAD2 is positively correlated with the progression of multiple cancer types, and poor patient outcomes. Although ATAD2 and ATAD2B are highly conserved, little is known about the function of ATAD2B, or its role in oncogenesis. We hypothesized that the ATAD2B bromodomain would likely be involved in recognition of di-acetyllysine modifications on the histone tail, similarly to its ATAD2 paralog. We identified the acetylated histone ligands of the ATAD2B bromodomain using a combination of isothermal titration calorimetry and nuclear magnetic resonance techniques. Interestingly, the ATAD2B bromodomain has different substrate specificity than the ATAD2 bromodomain, preferentially selecting for the histone H4K5acK8ac ligand. NMR chemical shift perturbation assays and site-directed mutagenesis were used to map out the acetyllysine binding pocket, enabling characterization of residues involved in coordination of mono- and di-acetylated histone ligands by the ATAD2B bromodomain. In addition, the X-ray crystal structure of the ATAD2B bromodomain in complex with an ATAD2 bromodomain inhibitor was solved at 2.2 Å resolution. This structure revealed that critical contacts required for bromodomain inhibitor coordination are conserved between the ATAD2/B bromodomains, and many of these residues play a dual role in acetyllysine recognition.

Structural insights into the recognition of mono- and di-acetyllysine by the ATAD2B bromodomain