Substrate Affinity and Specificity of the ScSth1p Bromodomain Are Fine-Tuned for Versatile Histone Recognition

Abstract

Bromodomains recognize a wide range of acetylated lysine residues in histones and other nuclear proteins. Substrate specificity is critical for their biological function and arises from unique acetyl-lysine binding sites formed by variable loop regions. Here, we analyzed substrate affinity and specificity of the yeast ScSth1p bromodomain, an essential component of the "Remodels the Structure of Chromatin" complex, and found that the wild-type bromodomain preferentially recognizes H3K14ac and H4K20ac peptides. Mutagenesis studies--guided by our crystal structure determined at 2.7 [A] resolution--revealed loop residues Ser1276 and Trp1338 as key determinants for such interactions. Strikingly, point mutations of each of these residues substantially increased peptide binding affinity and selectivity, respectively. Our data demonstrate that the ScSth1p bromodomain is not optimized for binding to an individual acetylation mark, but fine-tuned for interactions with several such modifications, consistent with the versatile and multivalent nature of histone recognition by reader modules such as bromodomains. HighlightsO_LIThe ScSth1p bromodomain preferentially recognizes H3K14ac and H4K20ac peptides C_LIO_LISer1276 and Trp1338 are key determinants of substrate affinity and specificity C_LIO_LIMutations of these residues drastically increase substrate affinity and specificity C_LIO_LIThe ScSth1p bromodomain is fine-tuned for promiscuous histone tail recognition C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/559005v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@10c54b3org.highwire.dtl.DTLVardef@8cb555org.highwire.dtl.DTLVardef@1d4ef1eorg.highwire.dtl.DTLVardef@9eaf00_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG