Wikipedia

EGLN1

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.[5][6][7][8] 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.

EGLN1
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesEGLN1, C1orf12, ECYT3, HIF-PH2, HIFPH2, HPH-2, HPH2, PHD2, SM20, ZMYND6, HALAH, egl-9 family hypoxia inducible factor 1
External IDsOMIM: 606425; MGI: 1932286; HomoloGene: 56936; GeneCards: EGLN1; OMA:EGLN1 - orthologs
Orthologs
SpeciesHumanMouse
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 MbChr 8: 125.64 – 125.68 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

The hypoxia response

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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.[9] 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.[8]

Structure

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The iron binding site of PHD2.

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.[10] 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.[11] 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.[10]

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).[12][13] These two HIF substrates are usually represented by 19 amino acid long peptides in in vitro experiments.[14] 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.[11][15] 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.[11][15] Such conformational change was confirmed by NMR spectroscopy,[15] X-ray crystallography[11][15] and molecular dynamics calculations.[16] 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.[17] 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.[18] 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.[19] Studies have revealed that PHD2 has a KM for dioxygen slightly above its atmospheric concentration, and PHD2 is thought to be the most important sensor of the cell's oxygen status.[20]

Mechanism

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The enzyme incorporates one oxygen atom from dioxygen into the hydroxylated product, and one oxygen atom into the succinate coproduct.[21] 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.[11] A feedback regulation mechanism that involves the displacement of HIF-1α by hydroxylated HIF-1α when 2-oxoglutarate is limiting was also proposed.[22]

 
PHD2 acts as a dioxygenase to hydroxylate proline and convert 2-oxoglutarate to succinate.

Biological role and disease relevance

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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.[8]

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.[23] Other in vivo models showed tumor-suppressing activity for PHD2 in pancreatic cancer as well as liver cancer.[24][25] 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.[26]

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.[27]

As a therapeutic _target

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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.[9] 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.[28] On the other hand, screens of small-molecule chelators have revealed hydroxypyrones and hydroxypyridones as potential inhibitors for PHD2.[29] 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.[30] 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.[31] Gasotransmitters including carbon monoxide[32] and nitric oxide[33][34] are also inhibitors of PHD2 by competing with molecular oxygen for binding at the active site Fe(II) ion.

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000135766 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000031987 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ Dupuy D, Aubert I, Duperat VG, Petit J, Taine L, Stef M, Bloch B, Arveiler B (Nov 2000). "Mapping, characterization, and expression analysis of the SM-20 human homologue, c1orf12, and identification of a novel related gene, SCAND2". Genomics. 69 (3): 348–54. doi:10.1006/geno.2000.6343. PMID 11056053.
  6. ^ 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.
  7. ^ "Entrez Gene: EGLN1 egl nine homolog 1 (C. elegans)".
  8. ^ a b c Berra E, Benizri E, Ginouvès A, Volmat V, Roux D, Pouysségur J (Aug 2003). "HIF prolyl-hydroxylase 2 is the key oxygen sensor setting low steady-state levels of HIF-1α in normoxia". The EMBO Journal. 22 (16): 4082–4090. doi:10.1093/emboj/cdg392. PMC 175782. PMID 12912907.
  9. ^ a b William C, Nicholls L, Ratcliffe P, Pugh C, Maxwell P (2004). "The prolyl hydroxylase enzymes that act as oxygen sensors regulating destruction of hypoxia-inducible factor α". Advan. Enzyme Regul. 44: 75–92. doi:10.1016/j.advenzreg.2003.11.017. PMID 15581484.
  10. ^ a b McDonough M, Li V, Flashman E, Chowdhury R, Mohr C, Liénard ZJ, Oldham N, Clifton I, Lewis J, McNeill L, Kurzeja R, Hewitson K, Yang E, Jordan S, Syed R, Schofield C (Jun 2006). "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)". Proc Natl Acad Sci USA. 103 (26): 9814–9. Bibcode:2006PNAS..103.9814M. doi:10.1073/pnas.0601283103. PMC 1502536. PMID 16782814.
  11. ^ a b c d e Chowdhury R, McDonough M, Mecinović J, Loenarz C, Flashman E, Hewitson K, Domene C, Schofield C (Jul 2009). "Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases". Structure. 17 (7): 981–9. doi:10.1016/j.str.2009.06.002. PMID 19604478.
  12. ^ Illingworth CJ, Loenarz C, Schofield CJ, Domene C (Aug 2010). "Chemical basis for the selectivity of the von Hippel Lindau tumor suppressor pVHL for prolyl-hydroxylated HIF-1α". Biochemistry. 49 (32): 6936–6944. doi:10.1021/bi100358t. PMID 20695530.
  13. ^ Abboud MI, Chowdhury R, Leung IK, Lippl K, Loenarz C, Claridge TD, Schofield CJ (Aug 2018). "Studies on the Substrate Selectivity of the Hypoxia-Inducible Factor Prolyl Hydroxylase 2 Catalytic Domain". ChemBioChem. 19 (21): 2262–2267. doi:10.1002/cbic.201800246. hdl:11343/261073. PMID 30144273. S2CID 52078684.
  14. ^ Flashman E, Bagg EA, Chowdhury R, Mecinović J, Loenarz C, McDonough MA, Hewitson KS, Schofield CJ (Feb 2008). "Kinetic rationale for selectivity toward N- and C-terminal oxygen-dependent degradation domain substrates mediated by a loop region of hypoxia-inducible factor prolyl hydroxylases". J Biol Chem. 283 (7): 3808–3815. doi:10.1074/jbc.M707411200. PMID 18063574.
  15. ^ a b c d Chowdhury R, Leung IK, Tian YM, Abboud MI, Ge W, Domene C, Cantrelle FX, Landrieu I, Hardy AP, Pugh CW, Ratcliffe PJ, Claridge TD, Schofield CJ (Aug 2016). "Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases". Nat Commun. 7: 12673. Bibcode:2016NatCo...712673C. doi:10.1038/ncomms12673. PMC 5007464. PMID 27561929.
  16. ^ Wick CR, Lanig H, Jäger CM, Burzlaff N, Clark T (Nov 2012). "Structural insight into the prolyl hydroxylase PHD2: a molecular dynamics and DFT study". Eur J Inorg Chem. 2012 (31): 4973–4985. doi:10.1002/ejic.201200391.
  17. ^ McAllister TE, Yeh TL, Abboud MI, Leung IK, Hookway ES, King ON, Bhushan B, Williams ST, Hopkinson RJ, Muenzel M, Loik ND, Chowdhury R, Oppermann U, Claridge TD, Goto Y, Suga H, Schofield CJ, Kawamura A (2018). "Non-competitive cyclic peptides for _targeting enzyme-substrate complexes". Chem Sci. 9 (20): 4569–4578. doi:10.1039/C8SC00286J. PMC 5969509. PMID 29899950.
  18. ^ McNeill L, Flashman E, Buck M, Hewitson K, Clifton I, Jeschke G, Claridge T, Ehrismann D, Oldham N, Schofield C (Oct 2005). "Hypoxia-inducible factor prolyl hydroxylase 2 has a high affinity for ferrous iron and 2-oxoglutarate". Mol. Biosyst. 1 (4): 321–4. doi:10.1039/b511249b. PMID 16880998.
  19. ^ Ehrismann D, Flashman E, Genn DN, Mathioudakis N, Hewitson KS, Ratcliffe PJ, Schofield CJ (Jan 2007). "Studies on the activity of the hypoxia-inducible-factor hydroxylases using an oxygen consumption assay". Biochem. J. 401 (1): 227–34. doi:10.1042/BJ20061151. PMC 1698668. PMID 16952279.
  20. ^ Hirsilä M, Koivunen P, Günzler V, Kivirikko KI, Myllyharju J (Aug 2003). "Characterization of the human prolyl 4-hydroxylases that modify the hypoxia-inducible factor". J. Biol. Chem. 278 (33): 30772–80. doi:10.1074/jbc.M304982200. PMID 12788921.
  21. ^ McNeill LA, Hewitson KS, Gleadle JM, Horsfall LE, Oldham NJ, Maxwell PH, Pugh CW, Ratcliffe PJ, Schofield CJ (Jun 2002). "The use of dioxygen by HIF prolyl hydroxylase (PHD1)". Bioorg. Med. Chem. 12 (12): 1547–50. doi:10.1016/S0960-894X(02)00219-6. PMID 12039559.
  22. ^ Abboud MI, McAllister TE, Leung IK, Chowdhury R, Jorgensen C, Domene C, Mecinović J, Lippl K, Hancock RL, Hopkinson RJ, Kawamura A, Claridge TD, Schofield CJ (Mar 2018). "2-Oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2". Chem. Commun. 54 (25): 3130–3133. doi:10.1039/C8CC00387D. PMC 5885369. PMID 29522057.
  23. ^ Ameln AK, Muschter A, Mamlouk S, Kalucka J, Prade I, Franke K, Rezaei M, Poitz DM, Breier G, Wielockx B (May 2011). "Inhibition of HIF prolyl hydroxylase-2 blocks tumor growth in mice through the antiproliferative activity of TGFβ". Cancer Res. 71 (9): 3306–16. doi:10.1158/0008-5472.CAN-10-3838. PMID 21436457.
  24. ^ Su Y, Loos M, Giese N, Metzen E, Büchler MW, Friess H, Kornberg A, Büchler P (Feb 2012). "Prolyl hydroxylase-2 (PHD2) exerts tumor-suppressive activity in pancreatic cancer". Cancer. 118 (4): 960–72. doi:10.1002/cncr.26344. PMID 21792862. S2CID 24482234.
  25. ^ Heindryckx F, Kuchnio A, Casteleyn C, Coulon S, Olievier K, Colle I, Geerts A, Libbrecht L, Carmeliet P, Van Vlierberghe H (Jul 2012). "Effect of prolyl hydroxylase domain-2 haplodeficiency on the hepatocarcinogenesis in mice". J. Hepatol. 57 (1): 61–8. doi:10.1016/j.jhep.2012.02.021. PMID 22420978.
  26. ^ Kamphues C, Wittschieber D, Klauschen F, Kasajima A, Dietel M, Schmidt SC, Glanemann M, Bahra M, Neuhaus P, Weichert W, Stenzinger A (Jan 2012). "Prolyl hydroxylase domain 2 protein is a strong prognostic marker in human gastric cancer". Pathobiology. 79 (1): 11–17. doi:10.1159/000330170. PMID 22236543.
  27. ^ Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, Prchal JT, Ge R (Jul 2010). "Genetic evidence for high-altitude adaptation in Tibet". Science. 329 (5987): 72–5. Bibcode:2010Sci...329...72S. doi:10.1126/science.1189406. PMID 20466884. S2CID 45471238.
  28. ^ Chintala S, Najrana T, Toth K, Cao S, Durrani F, Pili R, Rustum Y (2012). "Prolyl hydroxylase 2 dependent and Von-Hippel-Lindau independent degradation of hypoxia-inducible factor 1 and 2 alpha by selenium in clear cell renal cell carcinoma leads to tumor growth inhibition". BMC Cancer. 12: 293. doi:10.1186/1471-2407-12-293. PMC 3466155. PMID 22804960.
  29. ^ Flagg SC, Martin CB, Taabazuing CY, Holmes BE, Knapp MJ (Aug 2012). "Screening chelating inhibitors of HIF-prolyl hydroxylase domain 2 (PHD2) and factor inhibiting HIF (FIH)". J. Inorg. Biochem. 113: 25–30. doi:10.1016/j.jinorgbio.2012.03.002. PMC 3525482. PMID 22687491.
  30. ^ Chan MC, Atasoylu O, Hodson E, Tumber A, Leung IK, Chowdhury R, Gómez-Pérez V, Demetriades M, Rydzik AM, Holt-Martyn J, Tian YM, Bishop T, Claridge TD, Kawamura A, Pugh CW, Ratcliffe PJ, Schofield CJ (Jul 2015). "Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain". PLOS ONE. 6 (10): e0132004. Bibcode:2015PLoSO..1032004C. doi:10.1371/journal.pone.0132004. PMC 4492579. PMID 26147748.
  31. ^ Kwon HS, Choi YK, Kim JW, Park YK, Yang EG, Ahn DR (Jul 2011). "Inhibition of a prolyl hydroxylase domain (PHD) by substrate analog peptides". Bioorg. Med. Chem. Lett. 21 (14): 4325–8. doi:10.1016/j.bmcl.2011.05.050. PMID 21665470.
  32. ^ Mbenza NM, Nasarudin N, Vadakkedath PG, Patel K, Ismail AZ, Hanif M, Wright LJ, Sarojini V, Hartinger CG, Leung IK (June 2021). "Carbon monoxide is an inhibitor of HIF prolyl hydroxylase domain 2". ChemBioChem. 22 (15): 2521–2525. doi:10.1002/cbic.202100181. hdl:11343/298654. PMID 34137488. S2CID 235460239.
  33. ^ Metzen E, Zhou J, Jelkmann W, Fandrey J, Brüne B (August 2003). "Nitric Oxide Impairs Normoxic Degradation of HIF-1α by Inhibition of Prolyl Hydroxylases". Molecular Biology of the Cell. 14 (8): 3470–3481. doi:10.1091/mbc.E02-12-0791. PMC 181582. PMID 12925778.
  34. ^ Berchner-Pfannschmidt U, Yamac H, Trinidad B, Fandrey J (January 2007). "Nitric oxide modulates oxygen sensing by hypoxia-inducible factor 1-dependent induction of prolyl hydroxylase 2". Journal of Biological Chemistry. 282 (3): 1788–1796. doi:10.1074/jbc.M607065200. PMID 17060326.

Further reading

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  • Overview of all the structural information available in the PDB for UniProt: Q9GZT9 (Egl nine homolog 1) at the PDBe-KB.
Retrieved from "https://en.wikipedia.org/w/index.php?title=EGLN1&oldid=1188025126"
  NODES
Association 1
Note 1