BACKGROUND: Brd2 is a transcriptional regulator and belongs to BET family, a 
less characterized novel class of bromodomain-containing proteins. Brd2 contains 
two tandem bromodomains (BD1 and BD2, 46% sequence identity) in the N-terminus 
and a conserved motif named ET (extra C-terminal) domain at the C-terminus that 
is also present in some other bromodomain proteins. The two bromodomains have 
been shown to bind the acetylated histone H4 and to be responsible for mitotic 
retention on chromosomes, which is probably a distinctive feature of BET family 
proteins. Although the crystal structure of Brd2 BD1 is reported, no structure 
features have been characterized for Brd2 BD2 and its interaction with 
acetylated histones.
RESULTS: Here we report the solution structure of human Brd2 BD2 determined by 
NMR. Although the overall fold resembles the bromodomains from other proteins, 
significant differences can be found in loop regions, especially in the ZA loop 
in which a two amino acids insertion is involved in an uncommon pi-helix, termed 
piD. The helix piD forms a portion of the acetyl-lysine binding site, which 
could be a structural characteristic of Brd2 BD2 and other BET bromodomains. 
Unlike Brd2 BD1, BD2 is monomeric in solution. With NMR perturbation studies, we 
have mapped the H4-AcK12 peptide binding interface on Brd2 BD2 and shown that 
the binding was with low affinity (2.9 mM) and in fast exchange. Using NMR and 
mutational analysis, we identified several residues important for the Brd2 
BD2-H4-AcK12 peptide interaction and probed the potential mechanism for the 
specific recognition of acetylated histone codes by Brd2 BD2.
CONCLUSION: Brd2 BD2 is monomeric in solution and dynamically interacts with 
H4-AcK12. The additional secondary elements in the long ZA loop may be a common 
characteristic of BET bromodomains. Surrounding the ligand-binding cavity, five 
aspartate residues form a negatively charged collar that serves as a secondary 
binding site for H4-AcK12. We suggest that Brd2 BD1 and BD2 may possess 
distinctive roles and cooperate to regulate Brd2 functions. The structure basis 
of Brd2 BD2 will help to further characterize the functions of Brd2 and its BET 
members.