PWWP domains and their modes of sensing DNA and histone methylated lysines

Abstract

Chromatin plays an important role in gene transcription control, cell cycle progression, recombination, DNA replication and repair. The fundamental unit of chromatin, the nucleosome, is formed by a DNA duplex wrapped around an octamer of histones. Histones are susceptible to various post-translational modifications, covalent alterations that change the chromatin status. Lysine methylation is one of the major post-translational modifications involved in the regulation of chromatin function. The PWWP domain is a member of the Royal superfamily that functions as a chromatin methylation reader by recognizing both DNA and histone methylated lysines. The PWWP domain three-dimensional structure is based on an N-terminal hydrophobic β-barrel responsible for histone methyl-lysine binding, and a C-terminal α-helical domain. In this review, we set out to discuss the most recent literature on PWWP domains, focusing on their structural features and the mechanisms by which they specifically recognize DNA and histone methylated lysines at the level of the nucleosome.

Keywords: Epigenetics; Histone; Lysine; Methylation; PWWP Domain.

Fig. 1

Sequence alignment of PWWP domains. Primary sequence alignment of PWWP domains with previously determined three-dimensional structures. The experimental secondary structure of mouse DNMT3b PWWP (1KHC) is depicted on top of the figure. The Pro-Trp-Trp-Pro sequence motif is highlighted by the black box. Purple boxes mark highly conserved residues, while green boxes mark similar residues. The aromatic cage residues that directly participate in histone methylated lysine binding and recognition are colored red. Sequence alignment was performed with ClustalW2

Fig. 2

The PWWP domain fold. Ribbon diagram of mouse DNMT3b PWWP domain three-dimensional structure (1KHC). a The PWWP domain fold can be subdivided into two distinct substructural motifs. The N-terminal β-barrel is represented in orange, while the C-terminal helical bundle is colored blue. b The Pro-Trp-Tro-Pro sequence motif is positioned in the beginning of strand β2 and displayed in sticks. Residue W245 of mouse DNMT3b PWWP is engaged in direct binding to histone methyl-lysines and is red, while other residues (S243, W244, 9246) are gray

Fig. 3

Structural diversity of the PWWP domain C-terminal helical bundle. The PWWP domain C-terminal substructure may contain two to six helices. a Ribbon diagram of mouse DNMT3b PWWP (1KHC) displaying its five α-helical bundle. b Ribbon diagram of human BRPF1 PWWP (2X35). c Ribbon diagram of human HDGF PWWP (1RI0). d Ribbon diagram of yeast Pdp1 PWWP (2L89). e Ribbon diagram of human LEDGF/p75 PWWP (2M16). The C-terminal substructures of BRPF1, HDGF, Pdp1, and LEDGF/p75 PWWP domains are composed of two α-helices connected by a loop. All C-terminal helical bundles are blue

Fig. 4

The PWWP domain DNA-binding interface. a Ribbon diagram of human HDGF PWWP three-dimensional structure (2B8A). The N-terminal β-barrel is colored orange, while the C-terminal helical bundle is blue. The HDGF PWWP structure is first represented in the same orientation as Fig. 2 and then rotated 180° about the y axis. b The HDGF PWWP–DNA interface. Residues that directly engage in DNA binding are green and labeled. c Surface representation of the HDGF PWWP structure (2B8A) highlighting the residues that compose the DNA-binding interface (green). d Electrostatics distribution of the HDGF PWWP structure showing that the DNA-binding surface is positively charged

Fig. 5

The PWWP domain histone methyl-lysine-binding aromatic cage. Ribbon diagram of human BRPF1:H3K36me3 peptide complex three-dimensional structure (2X4W). The N-terminal β-barrel is in orange, while the C-terminal helical bundle is blue. The H3K36me3-containing histone peptide is displayed in sticks and colored magenta. The residues that compose the BRPF1 PWWP aromatic cage (Y1096, Y1099, and F1147) responsible for binding H3K36me3 are represented in sticks and colored red

Fig. 6

Structural model of the LEDGF/p75 PWWP-nucleosome complex. (a) Ribbon diagram of the data-driven structural model of the LEDGF/p75 PWWP domain in complex with the nucleosome (3ZH1). Histones are colored gray, while nucleosomal DNA is shown in salmon. The N-terminal β-barrel of the LEDGF/p75 PWWP domain is colored orange, and the C-terminal helical bundle is colored blue. Histone H3 residues 31–42, harboring the K36 trimehthylation mark, are displayed in sticks and colored magenta (b) Same as in a rotated 180° about the x axis. (c) A zoom in on the LEDGF/p75 PWWP domain interaction with the nucleosomal particle. The aromatic cage residues Y18, W21, F44, which are directly engaged in H3K36me3 binding, are represented in sticks and colored red. In addition, residues K16, K38, K56, K73, R74, K75, which nonspecifically bind DNA, are represented in sticks and colored green