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 

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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
  • Primary Citation of Related Structures:  
    3HQR, 3HQU

  • 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 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
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)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens)
Explore Q9GZT9 
Go to UniProtKB:  Q9GZT9
PHAROS:  Q9GZT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZT9
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1 alphaB [auth S]17Homo sapiensMutation(s): 0 
Gene Names: HIF1A, BHLHE78, MOP1, PASD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q16665 (Homo sapiens)
Explore Q16665 
Go to UniProtKB:  Q16665
PHAROS:  Q16665
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16665
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 Ideal Coordinates CCD File 
D [auth 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 Ideal Coordinates CCD File 
C [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
UN9 BindingDB:  3HQU Kd: 80 (nM) from 1 assay(s)
IC50: min: 70, max: 7500 (nM) from 8 assay(s)
EC50: 7.90e+4 (nM) from 1 assay(s)
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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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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