Structural and Histone Binding Ability Characterizations of Human PWWP Domains

Hong Wu,Wolfram Tempel,Hong Zeng,Maria F Amaya,Yanming Wang,Ludmila Dombrovski,Chao Xu,Wei Qiu,Jinrong Min,Robert Lam,Petri Kursula

doi:10.1371/journal.pone.0018919

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.

Highlights

The PWWP domain was first identified as a structural motif of 100–130 amino acids in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein and named after the conserved motif Pro-TrpTrp-Pro in WHSC1
It was shown that the PWWP domain in PSIP1 displays affinity for DNA and chromatin and its chromatin binding ability is crucial for the HIV-1 integration [10,11]
The major difference between these different PWWP domains is localized on the insertion motif, which varies in length among the different PWWP domains

Summary

Introduction

The PWWP domain was first identified as a structural motif of 100–130 amino acids in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein and named after the conserved motif Pro-TrpTrp-Pro in WHSC1. The PWWP domains of the DNA methyltransfearses DNMT3A and DNMT3B are essential for targeting DNA methylation to heterochromatin regions through their chromatin binding ability [5,6]. HDGF exerts its transcription repressive effect through binding to a conserved DNA element in the promoter region of target genes [8], it was reported that it functioned as a nonspecific DNA-binding domain [9]. Another member of this subfamily, PSIP1 (PC4 and SFRS1 interacting protein 1), is a transcriptional coactivator and involved in lentiviral integration. 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

Methods

Results

Conclusion