2Y34

S-nitrosylated PHD2 (NO exposed) in complex with Fe(II) and UN9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Studies on the reaction of nitric oxide with the hypoxia-inducible factor prolyl hydroxylase domain 2 (EGLN1).

Chowdhury, R., Flashman, E., Mecinovic, J., Kramer, H.B., Kessler, B.M., Frapart, Y.M., Boucher, J.L., Clifton, I.J., McDonough, M.A., Schofield, C.J.

(2011) J Mol Biol 410: 268-279

  • DOI: 10.1016/j.jmb.2011.04.075
  • Primary Citation of Related Structures:  
    2Y34, 2Y33

  • PubMed Abstract: 

    • The hypoxic response in animals is mediated via the transcription factor hypoxia-inducible factor (HIF). An oxygen-sensing component of the HIF system is provided by Fe(II) and 2-oxoglutarate-dependent oxygenases that catalyse the posttranslational h ...

    The hypoxic response in animals is mediated via the transcription factor hypoxia-inducible factor (HIF). An oxygen-sensing component of the HIF system is provided by Fe(II) and 2-oxoglutarate-dependent oxygenases that catalyse the posttranslational hydroxylation of the HIF-α subunit. It is proposed that the activity of the HIF hydroxylases can be regulated by their reaction with nitric oxide. We describe biochemical and biophysical studies on the reaction of prolyl hydroxylase domain-containing enzyme (PHD) isoform 2 (EGLN1) with nitric oxide and a nitric oxide transfer reagent. The combined results reveal the potential for the catalytic domain of PHD2 to react with nitric oxide both at its Fe(II) and at cysteine residues. Although the biological significance is unclear, the results suggest that the reaction of PHD2 with nitric oxide has the potential to be complex and are consistent with proposals based on cellular studies that nitric oxide may regulate the hypoxic response by direct reaction with the HIF hydroxylases.

    Related Citations: 
    • 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
    • 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: 

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EGL NINE HOMOLOG 1A252Homo sapiensMutation(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
Protein Feature View
Expand
  • 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SNC
Query on SNC		AL-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UN9IC50:  70   nM  BindingDB
UN9IC50:  73   nM  BindingDB
UN9IC50:  300   nM  BindingDB
UN9Kd :  80   nM  PDBBind
UN9IC50:  1400   nM  BindingDB
UN9Kd:  80   nM  BindingDB
UN9IC50:  424   nM  BindingDB
UN9IC50:  7500   nM  BindingDB
UN9IC50:  3900   nM  BindingDB
UN9EC50:  79000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.302α = 90
b = 110.302β = 90
c = 40.378γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-06-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-01-30
    Changes: Data collection, Experimental preparation