Structural and Histone Binding Ability Characterizations of Human PWWP Domains

Abstract

BackgroundThe PWWP domain was first identified as a structural motif of 100–130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain ‘Royal Family’, which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently.Methodology/Principal FindingsThe PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other ‘Royal Family’ members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3.ConclusionsPWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical β-barrel core, an insertion motif between the second and third β-strands and a C-terminal α-helix bundle. Both the canonical β-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

“…This is close to but slightly further into the gene body than where the mammalian homolog MOZ/MORF is predominantly found, 400 bp downstream of the TSS (Lalonde et al 2013). This 59 shift in MOZ/MORF localization could be due to the mammalian complex's reduced affinity for H3K4me1 (Champagne et al 2008) (Table S1) and H3K36me3 (Vezzoli et al 2010;Wu et al 2011) (Table S1), resulting in a much greater dependence on H3K4me2/3 for recruitment to chromatin. The differing methyl-histonebinding properties of NuA3 and MOZ/MORF coincide with differing genome-wide localization of H3K4me1 and H3K36me3.…”

Histone Variant H3.3: A versatile H3 variant in health and in disease

“…H3K36me3 and SETD2 have been demonstrated to regulate both transcriptional elongation and alternative splicing events (Wagner and Carpenter, 2012). Several proteins have been reported to read H3K36me3 modifications by virtue of possessing a PWWP domain, including DNMT3a and Brpf1 (Dhayalan et al, 2010;Vezzoli et al, 2010;Wu et al, 2011). A recent report described for the first time, a reader for H3.3-specific K36me3 called BS69/ZMYND11 (Wen et al, 2014c).…”

Histone H3.3 and cancer: A potential reader connection

“…It is also worth noting that the majority of previously identified readers and enzymes were discovered using H3.1 histone substrates. For instance, from a focused structure and thermodynamics study, several PWWP domains were reported to bind H3.1K36me3 but with very low affinity (K D values in the mM range) (65). These observations collectively raise the possibility that some of these readers could have a higher affinity for variant histones and are in fact variant histone binders.…”