Abstract
The plant homeodomain (PHD) zinc finger is a structural motif of about 40–60 amino acid residues found in many eukaryotic proteins that are involved in chromatin-mediated gene regulation. The human chromodomain helicase DNA binding protein 4 (CHD4) is a multi-domain protein that harbours, at its N-terminal end, a pair of PHD finger motifs (dPHD) connected by a ~30 amino acid linker. This tandem PHD motif is thought to be involved in targeting CHD4 to chromatin via its interaction with histone tails. Here we report the 1H, 13C and 15N backbone and side-chain resonance assignment of the entire dPHD by heteronuclear multidimensional NMR spectroscopy. These assignments provide the starting point for the determination of the structure, dynamics and histone-binding properties of this tandem domain pair.
Highlights
The plant homeodomain (PHD) zinc finger is a structural motif of about 40–60 amino acid residues found in many eukaryotic proteins that are involved in chromatinmediated gene regulation
The human chromodomain helicase DNA binding protein 4 (CHD4) is a multi-domain protein that harbours, at its N-terminal end, a pair of PHD finger motifs connected by a *30 amino acid linker. This tandem PHD motif is thought to be involved in targeting CHD4 to chromatin via its interaction with histone tails
In addition to its SNF2-type ATPase motor, CHD4 harbours double PHD fingers and double chromodomains (Fig. 1) that are believed to be involved in its targeting to the chromatin (Morra et al 2012), yet their mechanism of action is unclear
Summary
Plant homeodomain (PHD) fingers are short (*40–60 amino acid) protein domains which contain two zinc ions. In addition to its SNF2-type ATPase motor, CHD4 harbours double PHD fingers (dPHD) and double chromodomains (dCHD) (Fig. 1) that are believed to be involved in its targeting to the chromatin (Morra et al 2012), yet their mechanism of action is unclear. While the combination of PHD domains with other chromatin ‘‘reader’’ modules such as bromodomains is a feature of many chromatin-remodelling factors, the presence of tandem PHDs is characteristic of a much smaller subset of proteins including CHD4, CHD3, CHD5 and DPF3b. The structural mechanism of the acetylated histone binding by the double PHD fingers of DPF3b has been recently elucidated (Zeng et al 2010) and represents the first solution structure of a tandem PHD finger. Size exclusion chromatography in 20 mM Tris pH 7.5, 200 mM NaCl and 1–10 mM DTT
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