Hypoxia-Inducible Factors

HIF-1α is a molecular switch that responds to changing oxygen levels.

Complex of a peptide from HIF-1α (pink, with proline in red), pVHL (blue), and two elongins (green). The inset shows a close-up of the hydroxylated proline.
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Oxygen is essential--without it, our cells rapidly die. Because of this, our cells have a dedicated system that monitors the amount of oxygen, and mobilizes a variety of responses if the levels get too low. For example, when oxygen is scarce, this system shuts down pyruvate dehydrogenase and activates lactate dehydrogenase, shifting energy production towards pathways that don’t need oxygen. Oxygen-starved cells also send out signals that tell the body to create more blood cells and build more blood vessels. The Nobel Prize for Physiology or Medicine was awarded this year to three researchers who discovered the molecular details of this central oxygen-sensing process.

High Oxygen

Hypoxia-inducible factor 1α (HIF-1α) is the central switch that tells cells if they have enough oxygen or not. It is a protein with about 800 amino acids, with several functional parts. The structure shown here (PDB entry 1lqb) includes a small portion from the center, which has a key proline amino acid. When oxygen is plentiful, this proline is hydroxylated by the enzyme PHD2 (HIF prolyl hydroxylase 2, see below), along with a second proline nearby in the chain. The hydroxyproline is then recognized by pVHL (von Hipple-Lindau disease tumor suppressor), which is in turn recognized by elongin proteins that deliver HIF-1α to the ubiquitination machinery. Finally, HIF-1α is degraded by proteasomes, and the cell continues with its normal, oxygen-rich life.

Sensing Oxygen

PHD2 has the job of sensing oxygen levels. It is a small enzyme that attaches oxygen to two prolines in HIF-1α using a metal ion and the cofactor α-ketoglutarate to assist with the reaction. When oxygen is scarce, the enzyme can’t perform the reaction, and the prolines are not modified. An additional system, termed FIH (factor inhibiting HIF), performs a second type of hydroxylation reaction, targeting an asparagine in HIF-1α and modifying the way it interacts with the transcriptional machinery.

Complex of HIF-1α (pink), HIF-1β (yellow), and DNA (blue).
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Low Oxygen

When oxygen is low, HIF-1α is not hydroxylated and not degraded by proteasomes, so it springs into action. It moves to the nucleus and associates with a companion protein, called HIF-1β. Together, they bind to many sites in the genome and promote transcription of genes involved in low-oxygen metabolism and remodeling the circulatory system to improve oxygen delivery. The structure shown here (PDB entry 4zpr) includes the DNA-binding portion of the complex bound to a short piece of DNA.

Exploring the Structure

PHD2 Complexes

PHD2 has the job of hydroxylating HIF-1α. Several drugs that bind to PHD2 are currently being evaluated for the treatment of anemia. By blocking the enzyme, the drug tricks cells into thinking they need more oxygen, so they send signals to build more blood cells. One of these drugs, Vadadustat, is shown here (PDB entry 5ox6). By comparing this to the structure of HIF-1α bound to PHD2 (PDB entry 3hqr), we can see that the drug mimics the cofactor of the enzyme (NOG is similar to alpha-ketoglutarate), and is big enough to block binding the HIF-1α proline as well.

Topics for Further Discussion

  1. 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.
  2. The scissor-shaped DNA-binding domain of the HIF-1 complex is termed “basic helix-loop-helix.” You can see other examples by searching for “bHLH” on the main PDB site.


  1. 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.
  2. 4zpr: Wu, D., Potluri, N., Lu, J., Kim, Y., Rastinejad, F. (2015) Structural integration in hypoxia-inducible factors. Nature 524: 303-308.
  3. Semenza, G..L (2012) Hypoxia-inducible factors in physiology and medicine. Cell 148: 399-408.
  4. 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.
  5. 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.

December 2019, David Goodsell

About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. More