Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.74 kDa 
• Atom Count: 1854 
• Residue Count: 216 
• Unique protein chains: 1

2Y34

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

• DOI: 10.2210/pdb2Y34/pdb

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


• Deposited: 2010-12-18 Released: 2010-12-29 
• Deposition Author(s): Chowdhury, R., McDonough, M.A., Schofield, C.J.

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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 

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

• PubMed: 21601578 
• DOI: 10.1016/j.jmb.2011.04.075
• Structures With Same Primary Citation


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
EGL NINE HOMOLOG 1	A	252	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) 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
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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNC	A	L-PEPTIDE LINKING	C3 H6 N2 O3 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
UN9	IC50:  70   nM  BindingDB
UN9	IC50:  73   nM  BindingDB
UN9	IC50:  300   nM  BindingDB
UN9	Kd :  80   nM  PDBBind
UN9	IC50:  1400   nM  BindingDB
UN9	Kd:  80   nM  BindingDB
UN9	IC50:  424   nM  BindingDB
UN9	IC50:  3900   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 = 110.302	α = 90
b = 110.302	β = 90
c = 40.378	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-18 
• Released Date: 2010-12-29 
Deposition Author(s): Chowdhury, R., McDonough, M.A., Schofield, C.J.

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