Molecule of the Month: Hypoxia-Inducible Factors
HIF-α is a molecular switch that responds to changing oxygen levels.
Exploring the Structure
Drugs that bind to the PHD enzymes are being evaluated for treatment of anemia. By blocking these enzymes, the drug tricks cells into thinking they need more oxygen, so they send signals to build more red blood cells. Initial structures of PHD2 enabled structure-based design of inhibitors of the enzyme (PDB entries 2g1m, 2g19), and a drug currently under evaluation, vadadustat, is shown here (PDB entry 5ox6). By comparing this to the structure of PHD2 bound to a small piece of HIF-α (PDB entry 3hqr), we can see that the investigational drug mimics binding of α-ketoglutarate to the enzyme (NOG is similar to α-ketoglutarate), and is big enough to block binding of the HIF-α proline.
Topics for Further Discussion
- There are many structures of FIH (factor inhibiting HIF) in the PDB archive if you would like to explore it and its interaction with substrates and inhibitors.
- The scissor-shaped DNA-binding domain of the HIF complex is termed “basic helix-loop-helix.” You can see other examples by searching for “bHLH” on the main PDB site.
Related PDB-101 Resources
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- 5ox6: Yeh, T.L., Leissing, T.M., Abboud, M.I., Thinnes, C.C., Atasoylu, O., Holt-Martyn, J.P., Zhang, D., Tumber, A., Lippl, K., Lohans, C.T., Leung, I.K.H., Morcrette, H., Clifton, I.J., Claridge, T.D.W., Kawamura, A., Flashman, E., Lu, X., Ratcliffe, P.J., Chowdhury, R., Pugh, C.W., Schofield, C.J. (2017) Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials. Chem Sci 8: 7651-7668.
- 4zpr: Wu, D., Potluri, N., Lu, J., Kim, Y., Rastinejad, F. (2015) Structural integration in hypoxia-inducible factors. Nature 524: 303-308.
- Semenza, G..L (2012) Hypoxia-inducible factors in physiology and medicine. Cell 148: 399-408.
- 3hqr: Chowdhury, R., McDonough, M.A., Mecinovic, J., Loenarz, C., Flashman, E., Hewitson, K.S., Domene, C., Schofield, C.J. (2009) Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases. Structure 17: 981-989.
- 2g1m, 2g19: McDonough, M.A., Li, V., Flashman, E., Chowdhury, R., Mohr, C., Lienard, B.M.R., Zondlo, J., Oldham, N.J., Clifton, I.J., Lewis, J., McNeill, L.A., Kurzeja, R.J.M., Hewitson, K.S., Yang, E., Jordan, S., Syed, R.S., Schofield, C.J. (2006) Cellular oxygen sensing: crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2). Proc.Natl.Acad.Sci.USA 103: 9814-9819.
- 1h2n: Elkins, J.M., Hewitson, K.S., McNeill, L.A., Seibel, J.F., Schlemminger, I., Pugh, C., Ratcliffe, P., Schofield, C.J. (2003) Structure of factor-inhibiting hypoxia-inducible factor (Hif) reveals mechanism of oxidative modification of Hif-1Alpha. J.Biol.Chem. 278: 1802-1806.
- 1lqb: Hon, W.C., Wilson, M.I., Harlos, K., Claridge, T.D., Schofield, C.J., Pugh, C.W., Maxwell, P.H., Ratcliffe, P.J., Stuart, D.I., Jones, E.Y. (2002) Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL. Nature 417: 975-978.
- 1lm8: Min, J.H., Yang, H., Ivan, M., Gertler, F., Kaelin Jr., W.G., Pavletich, N.P. (2002) Structure of an HIF-1alpha -pVHL complex: hydroxyproline recognition in signaling. Science 296: 1886-1889
December 2019, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2019_12