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)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.721 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1042/BJ20140779

  • 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; thei ...

    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.


    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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EGL NINE HOMOLOG 1
A
252Homo sapiensMutation(s): 1 
Gene Names: EGLN1 (C1orf12)
EC: 1.14.11.29
Find proteins for Q9GZT9 (Homo sapiens)
Go to Gene View: EGLN1
Go to UniProtKB:  Q9GZT9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UN9
Query on UN9

Download SDF File 
Download CCD File 
A
N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
C12 H9 Cl N2 O4
OUQVKRKGTAUJQA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UN9IC50: 70 - 3900 nM (99) BINDINGDB
UN9Kd: 80 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.721 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 110.520α = 90.00
b = 110.520β = 90.00
c = 39.380γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Atomic model, Other
  • Version 1.2: 2014-10-22
    Type: Database references