3HQU

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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-L ...

    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.

    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
    Organizational Affiliation: 

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Egl nine homolog 1A246Homo sapiensMutation(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)
Explore Q9GZT9 
Go to UniProtKB:  Q9GZT9
NIH Common Fund Data Resources
PHAROS  Q9GZT9
GTEx  ENSG00000135766
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hypoxia-inducible factor 1 alphaS17Homo sapiensMutation(s): 0 
Gene Names: HIF1A, BHLHE78, MOP1, PASD8
Find proteins for Q16665 (Homo sapiens)
Explore Q16665 
Go to UniProtKB:  Q16665
NIH Common Fund Data Resources
PHAROS  Q16665
GTEx  ENSG00000100644
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UN9
Query on UN9
Download CCD File 
A
N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
C12 H9 Cl N2 O4
OUQVKRKGTAUJQA-UHFFFAOYSA-N		 Ligand Interaction
FE2
Query on FE2
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UN9IC50:  1400   nM  BindingDB
UN9IC50:  73   nM  BindingDB
UN9IC50:  300   nM  BindingDB
UN9IC50:  70   nM  BindingDB
UN9Kd:  80   nM  BindingDB
UN9IC50:  3900   nM  BindingDB
UN9IC50:  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 = 110.819α = 90
b = 110.819β = 90
c = 39.615γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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