Table 1. Non-HIF substrates tested in assays of PHD-catalysed hydroxylation.
Potential target proline residues in the proposed substrate (Gene ID, column 1) have been defined according to the sequence numbering of the canonical proteoform (Uniprot Accession, column 2).
Table 1—source data 1. Synthetic peptides tested in assays of PHD-catalysed hydroxylation.
Reported prolyl hydroxylation sites are indicated in red.
elife-46490-table1-data1.docx (29KB, docx)
DOI: 10.7554/eLife.46490.003
Table 1—source data 2. 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.
elife-46490-table1-data2.xlsx (47.5KB, xlsx)
DOI: 10.7554/eLife.46490.004
| Substrate | Uniprot Acc # | Target site(s) | PHD isoform | Reference |
|---|---|---|---|---|
| ACACB | O00763-1 | P343; P450; P2131 | PHD3 | German et al., 2016 |
| ACTB | P60709-1 | P307; P322 | PHD3 | Luo et al., 2014 |
| ADRB2 | P07550-1 | P382; P395 | PHD3 | Xie et al., 2009 |
| AKT1 | P31749-1 | P125; P313; P318; P423 | PHD2 | Guo et al., 2016 |
| ATF4 | P18848-1 | P156; P162; P164; P167; P174 | PHD3 | Köditz et al., 2007 |
| CENPN | Q96H22-1 | P311 | PHD2 | Moser et al., 2015 |
| CEP192 | Q8TEP8-3 | P2313 | PHD1 | Moser et al., 2013 |
| EEF2K | O00418-1 | P98 | Not defined | Moore et al., 2015 |
| EPOR | P19235-1 | P443; P450 | PHD3 | Heir et al., 2016 |
| FLNA | P21333-1 | P2317; P2324 | PHD2 | Segura et al., 2016 |
| FOXO3 | O43524-1 | P426; P437 | PHD1 | Zheng et al., 2014 |
| IKBKB | O14920-1 | P191 | PHD1 | Cummins et al., 2006 |
| MAPK6 | Q16659-1 | P25 | PHD3 | Rodriguez et al., 2016 |
| NDRG3 | Q9UGV2-1 | P294 | PHD2 | Lee et al., 2015 |
| PDE4D | Q08499-1 | P29; P382; P419 | PHD2 | Huo et al., 2012 |
| PKM | P14618-1 | P403; P408 | PHD3 | Luo et al., 2011 |
| POLR2A | P24928-1 | P1465 | PHD1 | Mikhaylova et al., 2008 |
| PPP2R2A | P63151-1 | P319 | PHD2 | Di Conza et al., 2017 |
| SPRY2 | O43597-1 | P18; P144; P160 | PHD1, 2, 3 | Anderson et al., 2011 |
| TELO2 | Q9Y4R8-1 | P374; P419; P422 | PHD3 | Xie et al., 2012 |
| THRA | P10827-1 | P160; P162 | PHD2, 3 | Xie et al., 2015 |
| TP53 | P04637-1 | P142 | PHD1 | Ullah et al., 2017 |
| TP53 | P04637-1 | P359 | PHD3 | Rodriguez et al., 2018 |
| TRPA1 | O75762-1 | P394 | PHD2 | Takahashi et al., 2011 |