NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3

Abstract

The plant homeodomain (PHD) modules are small 50–80 amino acid zinc fingers present in many nuclear proteins, which recognise histone post-translational modifications, i.e. lysine methylation and acetylation (Li and Li 2012; Musselman et al. 2012; Sanchez and Zhou 2011; Baker et al. 2008). These modifications play an essential role in the regulation of transcription, activation or repression depending on the nature and extent of the modification and on the target lysine. Misreading of these epigenetic marks has been related with many human pathological states, such as cancer, immunological and neurological diseases (Musselman et al. 2012; Baker et al. 2008). The death inducer obliterator (Dido) gene encodes three protein isoforms of different lengths. The longest and most broadly expressed, Dido3, is a nuclear protein that associates to the spindle pole in mitosis and to the synaptonemal complex in meiosis. Alterations in the expression of the Dido gene have been related to myeloid neoplasms in humans (Futterer et al. 2005). Based on pull-down assays, the N-terminal region of murine Dido3 has been reported to associate to histone H3 (Prieto et al. 2009). Histone recognition requires the PHD motif present in all Dido isoforms at their common N-terminal region (Fig. 1a; Prieto et al. 2009). It is noticeable that the PHD domain sequence in Dido genes from different organisms is completely conserved, whilst the overall identities lie in the range 60–96 %. Surface plasmon resonance experiments indicated that, in vitro, the Dido PHD domain is able to bind histone H3-derived peptides. The affinity is higher for the peptide with trimethylated-lysine 4 (H3K4me3) than for its non-methylated counterpart. Dido PHD domain was shown to recognise H3K4me3 also in vivo, and the methylation state of lysine 4 seems to be involved in the cellular localization of Dido3 (Prieto et al. 2009). Thus, knowledge of the molecular basis for the interaction between the PHD domain of Dido and histone H3K4me3 would improve current understanding of the biological roles played by Dido. With this aim in mind we proceeded to determine the structure of the PHD domain of Dido (DidoPHD), residues 265–322 in humans (Fig. 1a), and to map its interaction with a 12-residue H3K4me3 histone peptide (Fig. 1b).