PDBsum entry 3hqr

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Oxidoreductase/transcription PDB id
Protein chains
225 a.a. *
17 a.a. *
Waters ×151
* Residue conservation analysis
PDB id:
Name: Oxidoreductase/transcription
Title: Phd2:mn:nog:hif1-alpha substrate complex
Structure: Egl nine homolog 1. Chain: a. Fragment: phd2 catalytic domain, residues 181-426. Synonym: prolyl hydroxylase, 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. Mutation: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: phd2. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: peptide synthesis
2.00Å     R-factor:   0.234     R-free:   0.248
Authors: R.Chowdhury,M.A.Mcdonough,C.J.Schofield
Key ref:
R.Chowdhury et al. (2009). Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases. Structure, 17, 981-989. PubMed id: 19604478 DOI: 10.1016/j.str.2009.06.002
08-Jun-09     Release date:   28-Jul-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9GZT9  (EGLN1_HUMAN) -  Egl nine homolog 1
426 a.a.
225 a.a.*
Protein chain
Pfam   ArchSchema ?
Q16665  (HIF1A_HUMAN) -  Hypoxia-inducible factor 1-alpha
826 a.a.
17 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - 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
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  


DOI no: 10.1016/j.str.2009.06.002 Structure 17:981-989 (2009)
PubMed id: 19604478  
Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases.
R.Chowdhury, M.A.McDonough, J.Mecinović, C.Loenarz, E.Flashman, K.S.Hewitson, C.Domene, C.J.Schofield.
The oxygen-dependent hydroxylation of proline residues in the alpha subunit of hypoxia-inducible transcription factor (HIFalpha) is central to the hypoxic response in animals. Prolyl hydroxylation of HIFalpha increases its binding to the von Hippel-Lindau protein (pVHL), so signaling for degradation via the ubiquitin-proteasome system. The HIF prolyl hydroxylases (PHDs, prolyl hydroxylase domain enzymes) are related to the collagen prolyl hydroxylases, but form unusually stable complexes with their Fe(II) cofactor and 2-oxoglutarate cosubstrate. We report crystal structures of the catalytic domain of PHD2, the most important of the human PHDs, in complex with the C-terminal oxygen-dependent degradation domain of HIF-1alpha. Together with biochemical analyses, the results reveal that PHD catalysis involves a mobile region that isolates the hydroxylation site and stabilizes the PHD2.Fe(II).2OG complex. The results will be of use in the design of PHD inhibitors aimed at treating anemia and ischemic disease.
  Selected figure(s)  
Figure 2.
Figure 2. Conformational Changes in PHD2 Catalysis and Effect of PHD2 Variations on Activity and Selectivity
(A) Stereo view ribbons representation of the tPHD2.CODD complex structure. The tPHD2 fold comprises four α helices and ten β strands of which eight form a double-stranded β helix (DSBH, dark blue) (McDonough et al., 2006). Three of the four α helices (α1, α2, and α3) pack along the major β sheet and stabilize the DSBH.
(B) Stereo view ribbons representation of the tPHD2.CODD complex structure (green) superimposed with tPHD2.Fe(II).A structure (cyan) showing structural differences in the β2β3/loop (PHD2[237-254]) and C-terminal α4-helix conformations.
(C) Bicyclic inhibitors, such as A (salmon) disrupt the Arg-252:Asp-254 salt-bridge observed in the closed substrate binding conformation (P2[1]2[1]2[1]); they also apparently cause rotation of Tyr-310 C[β]-C[γ] (by vert, similar 45°) relative to that observed in the P6[3] form (not shown). Distances for selected salt bridges are given in angstroms.
(D) The tPHD2.CODD complex showing mutation sites (highlighted in white).
(E) 2OG turnover activity of wild-type (wt) and variant tPHD2 using NODD (blue) and CODD (red) substrates. 2OG turnover in absence of substrate was subtracted. Errors are standard deviations (n ≥ 3).
(F) Substrate hydroxylation and selectivity of wt and variant tPHD2 as determined by MALDI-TOF MS using CODD and NODD substrates.
Figure 3.
Figure 3. The Binding of Proline/Hydroxyproline Residues to PHD2 and VCB
(A and B) Comparisons of the Pro-564[CODD] conformations when bound to tPHD2 (A, green) and VCB (B, wheat). Superimposition of CODD (yellow)/ CODD[Hyp564] (purple) in complex with tPHD2 /VCB yielded rmsd of 2.6 Å for 14 residues (561–574, Cα atoms). The Pro-564[CODD] C^4-methylene is in the endo conformation when bound to tPHD2 and the exo conformation when Hyp-564[CODD] is bound to the VCB complex. The C^4 Pro-564 hydrogen(s) are modeled in black.
(C) Stereo view of coordination at the PHD2 (green) and the FIH (blue) active site; note the alternative position of the NOG 1-carboxylate. In the PHD2 structure, NOG (orange) chelates the metal via one of its carboxylate oxygens (O-Mn[II]; 2.4 Å; trans to His-374 N epsilon 2 (N2-Mn[II]; 1.9 Å) and its amide α-carbonyl oxygen (Oα-Mn(II); 2.1 Å; vert, similar trans to Asp-315 Oδ1; 2.0 Å). The metal-ligated water (in red) is positioned trans to His-313 (N epsilon 2-Mn[II]; 2.0 Å; H[2]O-Mn[II], 2.2 Å) and is positioned to hydrogen bond with Asp-315 Oδ2 (Oδ2-water; 2.4 Å).
  The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 981-989) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22343896 P.Koivunen, S.Lee, C.G.Duncan, G.Lopez, G.Lu, S.Ramkissoon, J.A.Losman, P.Joensuu, U.Bergmann, S.Gross, J.Travins, S.Weiss, R.Looper, K.L.Ligon, R.G.Verhaak, H.Yan, and W.G.Kaelin (2012).
Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation.
  Nature, 483, 484-488.  
21076780 A.Thalhammer, J.Mecinović, C.Loenarz, A.Tumber, N.R.Rose, T.D.Heightman, and C.J.Schofield (2011).
Inhibition of the histone demethylase JMJD2E by 3-substituted pyridine 2,4-dicarboxylates.
  Org Biomol Chem, 9, 127-135.  
20728359 C.Loenarz, and C.J.Schofield (2011).
Physiological and biochemical aspects of hydroxylations and demethylations catalyzed by human 2-oxoglutarate oxygenases.
  Trends Biochem Sci, 36, 7.  
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.  
21152646 D.Rotili, M.Altun, R.B.Hamed, C.Loenarz, A.Thalhammer, R.J.Hopkinson, Y.M.Tian, P.J.Ratcliffe, A.Mai, B.M.Kessler, and C.J.Schofield (2011).
Photoactivable peptides for identifying enzyme-substrate and protein-protein interactions.
  Chem Commun (Camb), 47, 1488-1490.  
20939709 F.S.Lee, and M.J.Percy (2011).
The HIF pathway and erythrocytosis.
  Annu Rev Pathol, 6, 165-192.  
21460794 R.Chowdhury, K.K.Yeoh, Y.M.Tian, L.Hillringhaus, E.A.Bagg, N.R.Rose, I.K.Leung, X.S.Li, E.C.Woon, M.Yang, M.A.McDonough, O.N.King, I.J.Clifton, R.J.Klose, T.D.Claridge, P.J.Ratcliffe, C.J.Schofield, and A.Kawamura (2011).
The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
  EMBO Rep, 12, 463-469.
PDB codes: 2ybk 2ybp 2ybs 2yc0 2yde
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.  
20199358 K.L.Gorres, and R.T.Raines (2010).
Prolyl 4-hydroxylase.
  Crit Rev Biochem Mol Biol, 45, 106-124.  
21209839 L.L.Hu, S.Niu, T.Huang, K.Wang, X.H.Shi, and Y.D.Cai (2010).
Prediction and analysis of protein hydroxyproline and hydroxylysine.
  PLoS One, 5, e15917.  
20416509 N.A.Smirnova, I.Rakhman, N.Moroz, M.Basso, J.Payappilly, S.Kazakov, F.Hernandez-Guzman, I.N.Gaisina, A.P.Kozikowski, R.R.Ratan, and I.G.Gazaryan (2010).
Utilization of an in vivo reporter for high throughput identification of branched small molecule regulators of hypoxic adaptation.
  Chem Biol, 17, 380-391.  
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
  20007141 R.van Wijk, S.Sutherland, A.C.Van Wesel, E.G.Huizinga, M.J.Percy, M.Bierings, and F.S.Lee (2010).
Erythrocytosis associated with a novel missense mutation in the HIF2A gene.
  Haematologica, 95, 829-832.  
19604469 T.D.Bugg (2009).
Oxygenases get to grips with polypeptides.
  Structure, 17, 913-914.  
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.