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EGLN1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2G19, 2G1M, 2HBT, 2HBU, 2Y33, 2Y34, 3HQR, 3HQU, 3OUH, 3OUI, 3OUJ, 4BQW, 4BQX, 4BQY, 4JZR, 4KBZ, 4UWD, 5A3U
Identifiers
Aliases	EGLN1, C1orf12, ECYT3, HIF-PH2, HIFPH2, HPH-2, HPH2, PHD2, SM20, ZMYND6, HALAH, egl-9 family hypoxia inducible factor 1
External IDs	OMIM: 606425; MGI: 1932286; HomoloGene: 56936; GeneCards: EGLN1; OMA:EGLN1 - orthologs
Gene location (Human) Chr. Chromosome 1 (human) Band 1q42.2 Start 231,363,751 bp End 231,422,287 bp
Gene location (Mouse) Chr. Chromosome 8 (mouse) Band 8|8 E2 Start 125,635,326 bp End 125,676,063 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in gastrocnemius muscle Achilles tendon muscle of thigh ventricular zone islet of Langerhans body of pancreas ganglionic eminence right auricle smooth muscle tissue left ventricle Top expressed in myocardium of ventricle digastric muscle cardiac muscle tissue of left ventricle interventricular septum right ventricle extraocular muscle plantaris muscle vastus lateralis muscle triceps brachii muscle extensor digitorum longus muscle More reference expression data BioGPS More reference expression data
Gene ontology Molecular function 2-oxoglutarate-dependent dioxygenase activity iron ion binding L-ascorbic acid binding dioxygenase activity metal ion binding protein binding oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline dioxygenase activity enzyme binding oxidoreductase activity peptidyl-proline 4-dioxygenase activity ferrous iron binding Cellular component cytoplasm nucleus cytosol postsynaptic density glutamatergic synapse Biological process response to hypoxia heart trabecula formation ventricular septum morphogenesis labyrinthine layer development response to nitric oxide peptidyl-proline hydroxylation to 4-hydroxy-L-proline cardiac muscle tissue morphogenesis regulation of angiogenesis negative regulation of DNA-binding transcription factor activity regulation of transcription from RNA polymerase II promoter in response to hypoxia negative regulation of cyclic-nucleotide phosphodiesterase activity oxygen homeostasis regulation of neuron death cellular iron ion homeostasis positive regulation of transcription by RNA polymerase II regulation of postsynapse organization regulation of protein catabolic process at postsynapse, modulating synaptic transmission Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 54583 112405 Ensembl ENSG00000135766 ENSMUSG00000031987 UniProt Q9GZT9 Q91YE3 RefSeq (mRNA) NM_022051 NM_001377260 NM_001377261 NM_053207 NM_001363475 RefSeq (protein) NP_071334 NP_444437 NP_001350404 Location (UCSC) Chr 1: 231.36 – 231.42 Mb Chr 8: 125.64 – 125.68 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

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Hypoxia-inducible factor prolyl hydroxylase 2 (HIF-PH2), or prolyl hydroxylase domain-containing protein 2 (PHD2), is an enzyme encoded by the EGLN1 gene. It is also known as Egl nine homolog 1. PHD2 is a α-ketoglutarate/2-oxoglutarate-dependent hydroxylase, a superfamily non-haem iron-containing proteins. In humans, PHD2 is one of the three isoforms of hypoxia-inducible factor-proline dioxygenase, which is also known as HIF prolyl-hydroxylase.

The hypoxia response

HIF-1α is a ubiquitous, constitutively synthesized transcription factor responsible for upregulating the expression of genes involved in the cellular response to hypoxia. These gene products may include proteins such as glycolytic enzymes and angiogenic growth factors. In normoxia, HIF alpha subunits are marked for the ubiquitin-proteasome degradation pathway through hydroxylation of proline-564 and proline-402 by PHD2. Prolyl hydroxylation is critical for promoting pVHL binding to HIF, which targets HIF for polyubiquitylation.

Structure

PHD2 is a 46-kDa enzyme that consists of an N-terminal domain homologous to MYND zinc finger domains, and a C-terminal domain homologous to the 2-oxoglutarate dioxygenases. The catalytic domain consists of a double-stranded β-helix core that is stabilized by three α-helices packed along the major β-sheet. The active site, which is contained in the pocket between the β-sheets, chelates iron(II) through histidine and aspartate coordination. 2-oxoglutarate displaces a water molecule to bind iron as well. The active site is lined by hydrophobic residues, possibly because such residues are less susceptible to potential oxidative damage by reactive species leaking from the iron center.

PHD2 catalyses the hydroxylation of two sites on HIF-α, which are termed the N-terminal oxygen dependent degradation domain (residues 395-413, NODD) and the C-terminal oxygen dependent degradation domain (residues 556-574, CODD). These two HIF substrates are usually represented by 19 amino acid long peptides in in vitro experiments. X-ray crystallography and NMR spectroscopy showed that both peptides bind to the same binding site on PHD2, in a cleft on the PHD2 surface. An induced fit mechanism was indicated from the structure, in which residues 237-254 adopt a closed loop conformation, whilst in the structure without CODD or NODD, the same residues adopted an open finger-like conformation. Such conformational change was confirmed by NMR spectroscopy, X-ray crystallography and molecular dynamics calculations. A recent study found a second peptide binding site on PHD2 although peptide binding to this alternative site did not seem to affect the catalytic activity of the enzyme. Further studies are required to fully understand the biological significance of this second peptide binding site.

The enzyme has a high affinity for iron(II) and 2-oxoglutarate (also known as α-ketoglutarate), and forms a long-lived complex with these factors. It has been proposed that cosubstrate and iron concentrations poise the HIF hydroxylases to respond to an appropriate "hypoxic window" for a particular cell type or tissue. Studies have revealed that PHD2 has a K_M for dioxygen slightly above its atmospheric concentration, and PHD2 is thought to be the most important sensor of the cell's oxygen status.

Mechanism

The enzyme incorporates one oxygen atom from dioxygen into the hydroxylated product, and one oxygen atom into the succinate coproduct. Its interactions with HIF-1α rely on a mobile loop region that helps to enclose the hydroxylation site and helps to stabilize binding of both iron and 2-oxyglutarate. A feedback regulation mechanism that involves the displacement of HIF-1α by hydroxylated HIF-1α when 2-oxoglutarate is limiting was also proposed.

Biological role and disease relevance

PHD2 is the primary regulator of HIF-1α steady state levels in the cell. A PHD2 knockdown showed increased levels of HIF-1α under normoxia, and an increase in HIF-1α nuclear accumulation and HIF-dependent transcription. HIF-1α steady state accumulation was dependent on the amount of PHD silencing effected by siRNA in HeLa cells and a variety of other human cell lines.

However, although it would seem that PHD2 downregulates HIF-1α and thus also tumorigenesis, there have been suggestions of paradoxical roles of PHD2 in tumor proliferation. For example, one animal study showed tumor reduction in PHD2-deficient mice through activation of antiproliferative TGF-β signaling. Other in vivo models showed tumor-suppressing activity for PHD2 in pancreatic cancer as well as liver cancer. A study of 121 human patients revealed PHD2 as a strong prognostic marker in gastric cancer, with PHD2-negative patients having shortened survival compared to PHD2-positive patients.

Recent genome-wide association studies have suggested that EGLN1 may be involved in the low hematocrit phenotype exhibited by the Tibetan population and hence that EGLN1 may play a role in the heritable adaptation of this population to live at high altitude.

As a therapeutic target

HIF's important role as a homeostatic mediator implicates PHD2 as a therapeutic target for a range of disorders regarding angiogenesis, erythropoeisis, and cellular proliferation. There has been interest both in potentiating and inhibiting the activity of PHD2. For example, methylselenocysteine (MSC) inhibition of HIF-1α led to tumor growth inhibition in renal cell carcinoma in a PHD-dependent manner. It is thought that this phenomenon relies on PHD-stabilization, but mechanistic details of this process have not yet been investigated. On the other hand, screens of small-molecule chelators have revealed hydroxypyrones and hydroxypyridones as potential inhibitors for PHD2. Recently, dihydropyrazoles, a triazole-based small molecule, was found to be a potent inhibitor of PHD2 that is active both in vitro and in vivo. Substrate analog peptides have also been developed to exhibit inhibitory selectivity for PHD2 over factor inhibiting HIF (FIH), for which some other PHD-inhibitors show overlapping specificity. Gasotransmitters including carbon monoxide and nitric oxide are also inhibitors of PHD2 by competing with molecular oxygen for binding at the active site Fe(II) ion.

References

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Further reading

• Semenza GL (2001). "HIF-1, O(2), and the 3 PHDs: how animal cells signal hypoxia to the nucleus". Cell. 107 (1): 1–3. doi:10.1016/S0092-8674(01)00518-9. PMID 11595178. S2CID 14922615.
• Wax SD, Tsao L, Lieb ME, et al. (1996). "SM-20 is a novel 40-kd protein whose expression in the arterial wall is restricted to smooth muscle". Lab. Invest. 74 (4): 797–808. PMID 8606489.
• Taylor MS (2001). "Characterization and comparative analysis of the EGLN gene family". Gene. 275 (1): 125–32. doi:10.1016/S0378-1119(01)00633-3. PMID 11574160.
• Epstein AC, Gleadle JM, McNeill LA, et al. (2001). "C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation". Cell. 107 (1): 43–54. doi:10.1016/S0092-8674(01)00507-4. PMID 11595184. S2CID 18372306.
• Oehme F, Ellinghaus P, Kolkhof P, et al. (2002). "Overexpression of PH-4, a novel putative proline 4-hydroxylase, modulates activity of hypoxia-inducible transcription factors". Biochem. Biophys. Res. Commun. 296 (2): 343–9. doi:10.1016/S0006-291X(02)00862-8. PMID 12163023.
• Ivan M, Haberberger T, Gervasi DC, et al. (2002). "Biochemical purification and pharmacological inhibition of a mammalian prolyl hydroxylase acting on hypoxia-inducible factor". Proc. Natl. Acad. Sci. U.S.A. 99 (21): 13459–64. Bibcode:2002PNAS...9913459I. doi:10.1073/pnas.192342099. PMC 129695. PMID 12351678.
• Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...9916899M. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
• Metzen E, Berchner-Pfannschmidt U, Stengel P, et al. (2003). "Intracellular localisation of human HIF-1 alpha hydroxylases: implications for oxygen sensing". J. Cell Sci. 116 (Pt 7): 1319–26. doi:10.1242/jcs.00318. PMID 12615973.
• Cioffi CL, Liu XQ, Kosinski PA, et al. (2003). "Differential regulation of HIF-1 alpha prolyl-4-hydroxylase genes by hypoxia in human cardiovascular cells". Biochem. Biophys. Res. Commun. 303 (3): 947–53. doi:10.1016/S0006-291X(03)00453-4. PMID 12670503.
• Aprelikova O, Chandramouli GV, Wood M, et al. (2004). "Regulation of HIF prolyl hydroxylases by hypoxia-inducible factors". J. Cell. Biochem. 92 (3): 491–501. doi:10.1002/jcb.20067. PMID 15156561. S2CID 24455956.
• Appelhoff RJ, Tian YM, Raval RR, et al. (2004). "Differential function of the prolyl hydroxylases PHD1, PHD2, and PHD3 in the regulation of hypoxia-inducible factor". J. Biol. Chem. 279 (37): 38458–65. doi:10.1074/jbc.M406026200. PMID 15247232.
• Metzen E, Stiehl DP, Doege K, et al. (2006). "Regulation of the prolyl hydroxylase domain protein 2 (phd2/egln-1) gene: identification of a functional hypoxia-responsive element". Biochem. J. 387 (Pt 3): 711–7. doi:10.1042/BJ20041736. PMC 1135001. PMID 15563275.
• Baek JH, Mahon PC, Oh J, et al. (2005). "OS-9 interacts with hypoxia-inducible factor 1alpha and prolyl hydroxylases to promote oxygen-dependent degradation of HIF-1alpha". Mol. Cell. 17 (4): 503–12. doi:10.1016/j.molcel.2005.01.011. PMID 15721254.
• Ozer A, Wu LC, Bruick RK (2005). "The candidate tumor suppressor ING4 represses activation of the hypoxia inducible factor (HIF)". Proc. Natl. Acad. Sci. U.S.A. 102 (21): 7481–6. Bibcode:2005PNAS..102.7481O. doi:10.1073/pnas.0502716102. PMC 1140452. PMID 15897452.
• Choi KO, Lee T, Lee N, et al. (2006). "Inhibition of the catalytic activity of hypoxia-inducible factor-1alpha-prolyl-hydroxylase 2 by a MYND-type zinc finger". Mol. Pharmacol. 68 (6): 1803–9. doi:10.1124/mol.105.015271. PMID 16155211. S2CID 6673747.
• To KK, Huang LE (2006). "SUPPRESSION OF HIF-1α TRANSCRIPTIONAL ACTIVITY BY THE HIF PROLYL HYDROXYLASE EGLN1". J. Biol. Chem. 280 (45): 38102–7. doi:10.1074/jbc.M504342200. PMC 1307502. PMID 16157596.
• Kato H, Inoue T, Asanoma K, et al. (2006). "Induction of human endometrial cancer cell senescence through modulation of HIF-1alpha activity by EGLN1". Int. J. Cancer. 118 (5): 1144–53. doi:10.1002/ijc.21488. PMID 16161047.

External links

• Overview of all the structural information available in the PDB for UniProt: Q9GZT9 (Egl nine homolog 1) at the PDBe-KB.

• Biology

• Genes on human chromosome 1
• Human 2OG oxygenases
• EC 1.14.11