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PDBsum entry 2g1m

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protein ligands metals links
Oxidoreductase PDB id
2g1m
Jmol
Contents
Protein chain
211 a.a. *
Ligands
4HG
Metals
FE2
Waters ×127
* Residue conservation analysis
PDB id:
2g1m
Name: Oxidoreductase
Title: Cellular oxygen sensing: crystal structure of hypoxia- inducible factor prolyl hydroxylase (phd2)
Structure: Egl nine homolog 1. Chain: a. Fragment: catalytic domain. Synonym: hypoxia-inducible factor prolyl hydroxylase 2, hif-prolyl hydroxylase 2, hif-ph2, hph-2, prolyl hydroxylase domain-containing protein 2, phd2, sm-20. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: egln1, c1orf12. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.216     R-free:   0.289
Authors: M.A.Mcdonough,C.J.Schofield
Key ref:
M.A.McDonough et al. (2006). Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2). Proc Natl Acad Sci U S A, 103, 9814-9819. PubMed id: 16782814 DOI: 10.1073/pnas.0601283103
Date:
14-Feb-06     Release date:   13-Jun-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9GZT9  (EGLN1_HUMAN) -  Egl nine homolog 1
Seq:
Struc:
426 a.a.
211 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.11.29  - Hypoxia-inducible factor-proline dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hypoxia-inducible factor-L-proline + 2-oxoglutarate + O2 = hypoxia- inducible factor-trans-4-hydroxy-L-proline + succinate + CO2
Hypoxia-inducible factor-L-proline
+ 2-oxoglutarate
+ O(2)
= hypoxia- inducible factor-trans-4-hydroxy-L-proline
+ succinate
+ CO(2)
      Cofactor: Fe(2+); L-ascorbate
Fe(2+)
L-ascorbate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0601283103 Proc Natl Acad Sci U S A 103:9814-9819 (2006)
PubMed id: 16782814  
 
 
Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2).
M.A.McDonough, V.Li, E.Flashman, R.Chowdhury, C.Mohr, B.M.Liénard, J.Zondlo, N.J.Oldham, I.J.Clifton, J.Lewis, L.A.McNeill, R.J.Kurzeja, K.S.Hewitson, E.Yang, S.Jordan, R.S.Syed, C.J.Schofield.
 
  ABSTRACT  
 
Cellular and physiological responses to changes in dioxygen levels in metazoans are mediated via the posttranslational oxidation of hypoxia-inducible transcription factor (HIF). Hydroxylation of conserved prolyl residues in the HIF-alpha subunit, catalyzed by HIF prolyl-hydroxylases (PHDs), signals for its proteasomal degradation. The requirement of the PHDs for dioxygen links changes in dioxygen levels with the transcriptional regulation of the gene array that enables the cellular response to chronic hypoxia; the PHDs thus act as an oxygen-sensing component of the HIF system, and their inhibition mimics the hypoxic response. We describe crystal structures of the catalytic domain of human PHD2, an important prolyl-4-hydroxylase in the human hypoxic response in normal cells, in complex with Fe(II) and an inhibitor to 1.7 A resolution. PHD2 crystallizes as a homotrimer and contains a double-stranded beta-helix core fold common to the Fe(II) and 2-oxoglutarate-dependant dioxygenase family, the residues of which are well conserved in the three human PHD enzymes (PHD 1-3). The structure provides insights into the hypoxic response, helps to rationalize a clinically observed mutation leading to familial erythrocytosis, and will aid in the design of PHD selective inhibitors for the treatment of anemia and ischemic disease.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The PHD reaction and an inhibitor. (a) PHD catalyzed prolyl-4-hydroxylation of HIF- ; one of the oxygens (red) from the dioxygen cosubstrate is incorporated into proline to form trans-4-hydroxyproline, and the other is incorporated into succinate. (b) The structure of compound A.
Figure 4.
Fig. 4. Surface representations of PHD2[cat] (a) and phytanoyl CoA hydroxylase (b) (21) comparing the entrances to the active site cavities. The surfaces are colored by depth with a gradient from blue (outermost) to orange (innermost).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21109780 C.Loenarz, M.L.Coleman, A.Boleininger, B.Schierwater, P.W.Holland, P.J.Ratcliffe, and C.J.Schofield (2011).
The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens.
  EMBO Rep, 12, 63-70.  
20959442 D.Astuti, C.J.Ricketts, R.Chowdhury, M.A.McDonough, D.Gentle, G.Kirby, S.Schlisio, R.S.Kenchappa, B.D.Carter, W.G.Kaelin, P.J.Ratcliffe, C.J.Schofield, F.Latif, and E.R.Maher (2011).
Mutation analysis of HIF prolyl hydroxylases (PHD/EGLN) in individuals with features of phaeochromocytoma and renal cell carcinoma susceptibility.
  Endocr Relat Cancer, 18, 73-83.  
19914348 C.M.West, Z.A.Wang, and H.van der Wel (2010).
A cytoplasmic prolyl hydroxylation and glycosylation pathway modifies Skp1 and regulates O2-dependent development in Dictyostelium.
  Biochim Biophys Acta, 1800, 160-171.  
  20205712 C.Wotzlaw, S.Gneuss, R.Konietzny, and J.Fandrey (2010).
Nanoscopy of the cellular response to hypoxia by means of fluorescence resonance energy transfer (FRET) and new FRET software.
  PMC Biophys, 3, 5.  
20840591 E.Flashman, L.M.Hoffart, R.B.Hamed, J.M.Bollinger, C.Krebs, and C.J.Schofield (2010).
Evidence for the slow reaction of hypoxia-inducible factor prolyl hydroxylase 2 with oxygen.
  FEBS J, 277, 4089-4099.  
20055761 E.Flashman, S.L.Davies, K.K.Yeoh, and C.J.Schofield (2010).
Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents.
  Biochem J, 427, 135-142.  
20040577 H.S.Kim, H.L.Kim, K.H.Kim, d.o. .J.Kim, S.J.Lee, J.Y.Yoon, H.J.Yoon, H.Y.Lee, S.B.Park, S.J.Kim, J.Y.Lee, and S.W.Suh (2010).
Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex.
  Nucleic Acids Res, 38, 2099-2110.
PDB codes: 3kt1 3kt4 3kt7
20199358 K.L.Gorres, and R.T.Raines (2010).
Prolyl 4-hydroxylase.
  Crit Rev Biochem Mol Biol, 45, 106-124.  
19947658 M.A.Culpepper, E.E.Scott, and J.Limburg (2010).
Crystal structure of prolyl 4-hydroxylase from Bacillus anthracis.
  Biochemistry, 49, 124-133.
PDB code: 3itq
20088513 N.R.Rose, E.C.Woon, G.L.Kingham, O.N.King, J.Mecinović, I.J.Clifton, S.S.Ng, J.Talib-Hardy, U.Oppermann, M.A.McDonough, and C.J.Schofield (2010).
Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometric screening and crystallographic approaches.
  J Med Chem, 53, 1810-1818.
PDB code: 2wwj
20095867 O.Weinreb, T.Amit, S.Mandel, L.Kupershmidt, and M.B.Youdim (2010).
Neuroprotective multifunctional iron chelators: from redox-sensitive process to novel therapeutic opportunities.
  Antioxid Redox Signal, 13, 919-949.  
19754349 S.Nagel, N.P.Talbot, J.Mecinović, T.G.Smith, A.M.Buchan, and C.J.Schofield (2010).
Therapeutic manipulation of the HIF hydroxylases.
  Antioxid Redox Signal, 12, 481-501.  
19880520 C.E.Charron, P.C.Chou, D.J.Coutts, V.Kumar, M.To, K.Akashi, L.Pinhu, M.Griffiths, I.M.Adcock, P.J.Barnes, and K.Ito (2009).
Hypoxia-inducible factor 1alpha induces corticosteroid-insensitive inflammation via reduction of histone deacetylase-2 transcription.
  J Biol Chem, 284, 36047-36054.  
19477431 D.A.Chan, T.L.Kawahara, P.D.Sutphin, H.Y.Chang, J.T.Chi, and A.J.Giaccia (2009).
Tumor vasculature is regulated by PHD2-mediated angiogenesis and bone marrow-derived cell recruitment.
  Cancer Cell, 15, 527-538.  
19494350 G.L.Semenza (2009).
Involvement of oxygen-sensing pathways in physiologic and pathologic erythropoiesis.
  Blood, 114, 2015-2019.  
19096759 H.Chen, and M.Costa (2009).
Iron- and 2-oxoglutarate-dependent dioxygenases: an emerging group of molecular targets for nickel toxicity and carcinogenicity.
  Biometals, 22, 191-196.  
19553701 M.K.Koski, R.Hieta, M.Hirsilä, A.Rönkä, J.Myllyharju, and R.K.Wierenga (2009).
The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif.
  J Biol Chem, 284, 25290-25301.
PDB code: 3gze
19074761 M.Kaczmarek, R.E.Cachau, I.A.Topol, K.S.Kasprzak, A.Ghio, and K.Salnikow (2009).
Metal Ions-Stimulated Iron Oxidation in Hydroxylases Facilitates Stabilization of HIF-1{alpha} Protein.
  Toxicol Sci, 107, 394-403.  
19147576 O.Aprelikova, S.Pandolfi, S.Tackett, M.Ferreira, K.Salnikow, Y.Ward, J.I.Risinger, J.C.Barrett, and J.Niederhuber (2009).
Melanoma antigen-11 inhibits the hypoxia-inducible factor prolyl hydroxylase 2 and activates hypoxic response.
  Cancer Res, 69, 616-624.  
19604478 R.Chowdhury, M.A.McDonough, J.Mecinović, C.Loenarz, E.Flashman, K.S.Hewitson, C.Domene, and C.J.Schofield (2009).
Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases.
  Structure, 17, 981-989.
PDB codes: 3hqr 3hqu
19546213 S.Barth, F.Edlich, U.Berchner-Pfannschmidt, S.Gneuss, G.Jahreis, P.A.Hasgall, J.Fandrey, R.H.Wenger, and G.Camenisch (2009).
Hypoxia-inducible factor prolyl-4-hydroxylase PHD2 protein abundance depends on integral membrane anchoring of FKBP38.
  J Biol Chem, 284, 23046-23058.  
19754880 S.Leitgeb, G.D.Straganz, and B.Nidetzky (2009).
Functional characterization of an orphan cupin protein from Burkholderia xenovorans reveals a mononuclear nonheme Fe2+-dependent oxygenase that cleaves beta-diketones.
  FEBS J, 276, 5983-5997.  
19604469 T.D.Bugg (2009).
Oxygenases get to grips with polypeptides.
  Structure, 17, 913-914.  
19698086 V.I.Bunik, and A.R.Fernie (2009).
Metabolic control exerted by the 2-oxoglutarate dehydrogenase reaction: a cross-kingdom comparison of the crossroad between energy production and nitrogen assimilation.
  Biochem J, 422, 405-421.  
19737748 Z.Shao, Y.Zhang, and J.A.Powell-Coffman (2009).
Two distinct roles for EGL-9 in the regulation of HIF-1-mediated gene expression in Caenorhabditis elegans.
  Genetics, 183, 821-829.  
18617893 B.Bleijlevens, T.Shivarattan, E.Flashman, Y.Yang, P.J.Simpson, P.Koivisto, B.Sedgwick, C.J.Schofield, and S.J.Matthews (2008).
Dynamic states of the DNA repair enzyme AlkB regulate product release.
  EMBO Rep, 9, 872-877.  
19048166 B.M.Lienard, A.Conejo-García, I.Stolze, C.Loenarz, N.J.Oldham, P.J.Ratcliffe, and C.J.Schofield (2008).
Evaluation of aspirin metabolites as inhibitors of hypoxia-inducible factor hydroxylases.
  Chem Commun (Camb), (), 6393-6395.  
18538455 F.S.Lee (2008).
Genetic causes of erythrocytosis and the oxygen-sensing pathway.
  Blood Rev, 22, 321-332.  
18259202 G.H.Fong, and K.Takeda (2008).
Role and regulation of prolyl hydroxylase domain proteins.
  Cell Death Differ, 15, 635-641.  
18813363 J.M.Simmons, T.A.Müller, and R.P.Hausinger (2008).
Fe(II)/alpha-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism.
  Dalton Trans, (), 5132-5142.  
18058781 J.Mecinović, R.Chowdhury, B.M.Liénard, E.Flashman, M.R.Buck, N.J.Oldham, and C.J.Schofield (2008).
ESI-MS studies on prolyl hydroxylase domain 2 reveal a new metal binding site.
  ChemMedChem, 3, 569-572.  
18424552 M.C.Lauzier, G.A.Robitaille, D.A.Chan, A.J.Giaccia, and D.E.Richard (2008).
(2R)-[(4-Biphenylylsulfonyl)amino]-N-hydroxy-3-phenylpropionamide (BiPS), a matrix metalloprotease inhibitor, is a novel and potent activator of hypoxia-inducible factors.
  Mol Pharmacol, 74, 282-288.  
18402654 M.L.Alcaide-German, A.Vara-Vega, L.F.Garcia-Fernandez, M.O.Landazuri, and L.del Peso (2008).
A yeast three-hybrid system that reconstitutes mammalian hypoxia inducible factor regulatory machinery.
  BMC Cell Biol, 9, 18.  
19020684 P.C.Bruijnincx, G.van Koten, and R.J.Klein Gebbink (2008).
Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
  Chem Soc Rev, 37, 2716-2744.  
18568157 R.Chowdhury, A.Hardy, and C.J.Schofield (2008).
The human oxygen sensing machinery and its manipulation.
  Chem Soc Rev, 37, 1308-1319.  
18710826 X.Y.Li, C.Takasaki, Y.Satoh, S.Kimura, K.Yasumoto, and K.Sogawa (2008).
Expression, purification and characterization of human PHD1 in Escherichia coli.
  J Biochem, 144, 555-561.  
17301803 A.Ozer, and R.K.Bruick (2007).
Non-heme dioxygenases: cellular sensors and regulators jelly rolled into one?
  Nat Chem Biol, 3, 144-153.  
17579185 M.J.Percy, P.W.Furlow, P.A.Beer, T.R.Lappin, M.F.McMullin, and F.S.Lee (2007).
A novel erythrocytosis-associated PHD2 mutation suggests the location of a HIF binding groove.
  Blood, 110, 2193-2196.  
17893032 T.P.Cash, Y.Pan, and M.C.Simon (2007).
Reactive oxygen species and cellular oxygen sensing.
  Free Radic Biol Med, 43, 1219-1225.  
17101781 Y.Pan, K.D.Mansfield, C.C.Bertozzi, V.Rudenko, D.A.Chan, A.J.Giaccia, and M.C.Simon (2007).
Multiple factors affecting cellular redox status and energy metabolism modulate hypoxia-inducible factor prolyl hydroxylase activity in vivo and in vitro.
  Mol Cell Biol, 27, 912-925.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.