Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.95 kDa 
• Atom Count: 1778 
• Residue Count: 211 
• Unique protein chains: 1

2G1M

Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2)

• DOI: 10.2210/pdb2G1M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-02-14 Released: 2006-06-13 
• Deposition Author(s): Mcdonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.289 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2).

McDonough, M.A., Li, V., Flashman, E., Chowdhury, R., Mohr, C., Lienard, B.M., Zondlo, J., Oldham, N.J., Clifton, I.J., Lewis, J., McNeill, L.A., Kurzeja, R.J., Hewitson, K.S., Yang, E., Jordan, S., Syed, R.S., Schofield, C.J.

(2006) Proc Natl Acad Sci U S A 103: 9814-9819

• PubMed: 16782814 
• DOI: 10.1073/pnas.0601283103
• Primary Citation of Related Structures:  
  2G1M, 2G19


• PubMed 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.

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Organizational Affiliation: 

Oxford Centre for Molecular Sciences and Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	246	Homo sapiens	Mutation(s): 0  Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11 (PDB Primary Data), 1.14.11.29 (UniProt)
Find proteins for Q9GZT9 (Homo sapiens) Explore Q9GZT9  Go to UniProtKB:  Q9GZT9
NIH Common Fund Data Resources
PHAROS  Q9GZT9 GTEx  ENSG00000135766

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4HG	A	N-[(4-HYDROXY-8-IODOISOQUINOLIN-3-YL)CARBONYL]GLYCINE C12 H9 I N2 O4 FUMNLXHPILGSLC-UHFFFAOYSA-N
FE2	A	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4HG	IC50:  1400   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.289 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.742	α = 90
b = 110.742	β = 90
c = 39.986	γ = 120

Software Package:

Software Name	Purpose
SAINT	data scaling
SADABS	data reduction
SOLVE	phasing
RESOLVE	model building
CNS	refinement
SAINT	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-14 
• Released Date: 2006-06-13 
Deposition Author(s): Mcdonough, M.A., Schofield, C.J.

Revision History 

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description