Although the plant homeodomain (PHD) finger superfamily is known for its site-specific readouts of histone tails, the origins of the mechanistic differences in histone H3 readout by different PHD subtypes remain less clear. We show that sequences containing the xCDxCDx motif in the PHD treble clef (xCDxCDx-PHD) constitute a distinct subtype, based on the following observations: (i) the amino acid composition of the binding site is strikingly different from other subtypes due to position-specific enrichment of negatively charged and bulky nonpolar residues, (ii) the binding site positions are mutually and positively correlated, and this correlation is absent in other subtypes, and (iii) there are only small structural deviations, despite low sequence similarity. The xCDxCDx-PHD constitutes ∼20% of the PHD family, and the double PHD fingers (DPFs) are 10% of the total number of xCDxCDx-PHDs. This subtype originated early in the evolution of eukaryotes but has diversified within the metazoan lineage. Despite sequence diversification, the positions of the enriched nonpolar residues, in particular, show very small structural deviations, suggesting critical contributions of nonpolar residues in the binding mechanism of this subtype. Using mutagenesis, we probed the contributions of the binding-site positions enriched in nonpolar residues in four xCDxCDx-PHD proteins and found that they contribute to the tight packing of the H3 residues. This effect may potentially be exploited, as we observed affinity enhancement upon substituting a bulky nonpolar residue at the same binding site in another histone reader. Overall, we present a detailed characterization of PHD subtypes.

中文翻译：

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PHD手指亚型的特征。

尽管植物同源域（PHD）手指超家族因其特定位置的组蛋白尾巴读数而闻名，但不同PHD亚型在组蛋白H3读数上的机械差异的起源仍不清楚。我们根据以下观察结果显示，在PHD高音谱号（xCDxCDx-PHD）中包含xCDxCDx主题的序列构成了一个独特的亚型：（i）由于位置-，结合位点的氨基酸组成与其他亚型显着不同带负电荷和庞大的非极性残基的特异性富集，（ii）结合位点位置相互正相关，而在其他亚型中则不存在这种相关性，并且（iii）尽管序列相似性低，但结构上的偏差很小。xCDxCDx-PHD约占PHD系列的20％，和双PHD手指（DPF）占xCDxCDx-PHD总数的10％。该亚型起源于真核生物的进化早期，但在后生动物谱系内已经多样化。尽管序列多样化，但是富集的非极性残基的位置尤其显示出非常小的结构偏差，表明非极性残基在该亚型的结合机制中起关键作用。使用诱变，我们探究了丰富的结合位点位置在四个xCDxCDx-PHD蛋白中的非极性残基的贡献，并发现它们有助于H3残基的紧密堆积。由于我们观察到在另一个组蛋白阅读器的相同结合位点上取代了笨重的非极性残基后，亲和力增强，因此可能会利用这种效应。全面的，