Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.45 kDa 
• Atom Count: 1962 
• Residue Count: 221 
• Unique protein chains: 1

4UWD

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) D315E VARIANT in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)

• DOI: 10.2210/pdb4UWD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-08-11 Released: 2014-08-27 
• Deposition Author(s): Chowdhury, R., Tarhonskaya, H., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.173 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Investigating the Contribution of the Active Site Environment to the Slow Reaction of Hypoxia-Inducible Factor Prolyl Hydroxylase Domain 2 with Oxygen.

Tarhonskaya, H., Chowdhury, R., Leung, I.K.H., Loik, N.D., Mccullagh, J.S.O., Claridge, T.D.W., Schofield, C.J., Flashman, E.

(2014) Biochem J 463: 363

• PubMed: 25120187 
• DOI: 10.1042/BJ20140779
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The prolyl hydroxylase domain proteins (PHDs) catalyse the post-translational hydroxylation of the hypoxia-inducible factor (HIF), a modification that regulates the hypoxic response in humans. The PHDs are Fe(II)/2-oxoglutarate (2OG) oxygenases; their catalysis is proposed to provide a link between cellular HIF levels and changes in O2 availability. Transient kinetic studies have shown that purified PHD2 reacts slowly with O2 compared with some other studied 2OG oxygenases, a property which may be related to its hypoxia-sensing role. PHD2 forms a stable complex with Fe(II) and 2OG; crystallographic and kinetic analyses indicate that an Fe(II)-co-ordinated water molecule, which must be displaced before O2 binding, is relatively stable in the active site of PHD2. We used active site substitutions to investigate whether these properties are related to the slow reaction of PHD2 with O2. While disruption of 2OG binding in a R383K variant did not accelerate O2 activation, we found that substitution of the Fe(II)-binding aspartate for a glutamate residue (D315E) manifested significantly reduced Fe(II) binding, yet maintained catalytic activity with a 5-fold faster reaction with O2. The results inform on how the precise active site environment of oxygenases can affect rates of O2 activation and provide insights into limiting steps in PHD catalysis.

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Related Citations: 

• Selective Small Molecule Probes for the Hypoxia Inducible Factor (Hif) Prolyl Hydroxylases.
  Chowdhury, R., Candela-Lena, J.I., Chan, M.C., Greenald, D.J., Yeoh, K.K., Tian, Y., Mcdonough, M.A., Tumber, A., Rose, N.R., Conejo-Garcia, A., Demetriades, M., Mathavan, S., Kawamura, A., Lee, M.K., Van Eeden, F., Pugh, C.W., Ratcliffe, P.J., Schofield, C.J.
  (2013) ACS Chem Biol 8: 1488

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Organizational Affiliation: 

*Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
EGL NINE HOMOLOG 1	A	252	Homo sapiens	Mutation(s): 1  Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11.2 (PDB Primary Data), 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
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.173 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.52	α = 90
b = 110.52	β = 90
c = 39.38	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-11 
• Released Date: 2014-08-27 
Deposition Author(s): Chowdhury, R., Tarhonskaya, H., Schofield, C.J.

Revision History 

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-09-10
  Changes: Atomic model, Other
• Version 1.2: 2014-10-22
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation