Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.89 kDa 
• Atom Count: 1908 
• Residue Count: 222 
• Unique protein chains: 2

3HQU

PHD2:Fe:UN9:partial HIF1-alpha substrate complex

• DOI: 10.2210/pdb3HQU/pdb

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


• Deposited: 2009-06-08 Released: 2009-07-28 
• Deposition Author(s): Chowdhury, R., McDonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 

Literature

Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases

Chowdhury, R., McDonough, M.A., Mecinovic, J., Loenarz, C., Flashman, E., Hewitson, K.S., Domene, C., Schofield, C.J.

(2009) Structure 17: 981-989

• PubMed: 19604478 
• DOI: 10.1016/j.str.2009.06.002
• Structures With Same Primary Citation


• PubMed Abstract: 
  

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.

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Related Citations: 

• 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.R., Zondlo, J., Oldham, N.J., Clifton, I.J., Lewis, J., McNeill, L.A., Kurzeja, R.J.M., Hewitson, K.S., Yang, E., Jordan, S., Syed, R.S., Schofield, C.J.
  (2006) Proc Natl Acad Sci U S A 103: 9814

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Organizational Affiliation: 

Department of Chemistry and Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Egl nine homolog 1	A	246	Homo sapiens	Mutation(s): 0  Gene Names: PHD2(amino acids 181-426), EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11 (PDB Primary Data), 1.14.11.29 (UniProt)
Find proteins for Q9GZT9 (Homo sapiens) Go to UniProtKB:  Q9GZT9
NIH Common Fund Data Resources
PHAROS  Q9GZT9 GTEx  ENSG00000135766

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hypoxia-inducible factor 1 alpha	S	17	Homo sapiens	Mutation(s): 0  Gene Names: HIF1A, BHLHE78, MOP1, PASD8
Find proteins for Q16665 (Homo sapiens) Go to UniProtKB:  Q16665
NIH Common Fund Data Resources
PHAROS  Q16665 GTEx  ENSG00000100644

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UN9	A	N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE C12 H9 Cl N2 O4 OUQVKRKGTAUJQA-UHFFFAOYSA-N
FE2	A	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
UN9	IC50:  1400   nM  BindingDB
UN9	IC50:  73   nM  BindingDB
UN9	IC50:  300   nM  BindingDB
UN9	IC50:  70   nM  BindingDB
UN9	Kd:  80   nM  BindingDB
UN9	IC50:  3900   nM  BindingDB
UN9	IC50:  424   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.819	α = 90
b = 110.819	β = 90
c = 39.615	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-08 
• Released Date: 2009-07-28 
Deposition Author(s): Chowdhury, R., McDonough, M.A., Schofield, C.J.

Revision History 

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description