Secondary structure comparison of HIF and non-HIF PHD substrates using crystallographic data and PSIPRED prediction software.
The secondary structures of metazoan HIF-α (upper panel) and reported non-HIF PHD substrates (human; lower panel) were predicted by PSIPRED (Jones, 1999) and, where possible, referenced to crystallographic data from the protein data bank (PDB). Predicted structural elements are defined as alpha-helical (red), beta-strand (blue), or coiled/no secondary structure (uncoloured). Note, PSIPRED does not define detailed secondary structures, such as bends/turns (green) and beta-bridges (start of a strand; yellow). Input sequences for PSIPRED were 30-mer in length with the target proline (bold) sited centrally. To limit duplication, for sequences containing multiple target residues in close proximity (i.e., less than five residues apart), only one sequence corresponding to the N-terminal target proline is shown. Metazoan HIF sequences which support human PHD2 catalytic activity in vitro are included (Loenarz et al., 2011): dr, Danio rerio; bf, Branchiostoma floridae; sp, Strongylocentrotus purpurtas; mm, Mus musculus; nv, Nasonia vitripensis; ta, Trichoplax adhaerens. Italicised PDB codes indicate substrates crystalized in complex with a PHD; ‘-' denotes end of resolved structure.