Crystal structure of the human SUV39H1 chromodomain and its recognition of histone H3K9me2/3

Abstract

SUV39H1, the first identified histone lysine methyltransferase in human, is involved in chromatin modification and gene regulation. SUV39H1 contains a chromodomain in its N-terminus, which potentially plays a role in methyl-lysine recognition and SUV39H1 targeting. In this study, the structure of the chromodomain of human SUV39H1 was determined by X-ray crystallography. The SUV39H1 chromodomain displays a generally conserved structure fold compared with other solved chromodomains. However, different from other chromodomains, the SUV39H1 chromodomain possesses a much longer helix at its C-terminus. Furthermore, the SUV39H1 chromodomain was shown to recognize histone H3K9me2/3 specifically.

Figure 1. Sequence alignment of chromodomains and the crystal structure of human SUV39H1 chromodomain.

A: Alignment of chromodomain sequences of human SUV39H1, human MPP8, Drosophila HP1, Drosophila polycomb protein and human chromobox homologs CBX3. HsSUV39H1, human SUV39H1 chromodomain; HsMPP8, human MPP8 chromodomain; DmHP1, Drosophila melanogaster HP1 chromodomain; DmPolycomb, Drosophila melanogaster polycomb protein chromodomain; HsCBX3, human chromobox homolog 3, HP1γ. Secondary structures of the SUV39H1 chromodomain are labeled at the top and the aromatic cage residues are marked by as well. B: The crystallographic asymmetric unit of human SUV39H1 chromodomain, colored in cyan, green and yellow, respectively. C: The ribbon diagram of human SUV39H1 chromodomain monomer colored in cyan and secondary structures are labeled.

Figure 2. Structural comparison between human SUV39H1 chromodomain and other chromodomains, which are all colored in cyan A: human SUV39H1 chromodomain (PDB ID: 3MTS).

B: human MPP8 chromodomain (PDB ID: 3R93) C: Drosophila HP1 chromodomain (PDB ID: 1KNE).

Figure 3. Kinetic analysis of interactions between SUV39H1 chromodomain and H3K9me3/2/1/0 or H3K27me3 peptide was performed by fluorescence polarization assay.

Diagrams of different H3 peptides are indicated by different symbols. A: Kinetic analysis of interactions between truncated SUV39H1 chromodomain (aa 44–106) and H3K9me3/2/1/0 peptide. B: Kinetic analysis of interactions between complete SUV39H1 chromodomain (aa 42–100) and H3K9me3/2/1/0 or H3K27me3 peptide.

Figure 4. Hypothetical model of H3K9me3 binding by human SUV39H1 chromodomain.

The structures of human SUV39H1 and Drosophila melanogaster HP1 (PDB: 1KNE) chromodomains are aligned and shown in magenta and cyan, respectively. Y24, W45 and Y48 of Drosophila melanogaster HP1 chromodomain that are critical for H3K9me3 binding are shown as sticks in blue. The corresponding residues, W64 and Y67 of human SUV39H1 chromodomain, are shown as sticks in red. H3K9me3 peptide is shown in yellow with trimethylated lysine 9 shown as sticks.