5L9R

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.

Chowdhury, R.Leung, I.K.Tian, Y.M.Abboud, M.I.Ge, W.Domene, C.Cantrelle, F.X.Landrieu, I.Hardy, A.P.Pugh, C.W.Ratcliffe, P.J.Claridge, T.D.Schofield, C.J.

(2016) Nat Commun 7: 12673-12673

  • DOI: 10.1038/ncomms12673
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The response to hypoxia in animals involves the expression of multiple genes regulated by the αβ-hypoxia-inducible transcription factors (HIFs). The hypoxia-sensing mechanism involves oxygen limited hydroxylation of prolyl residues in the N- and C-te ...

    The response to hypoxia in animals involves the expression of multiple genes regulated by the αβ-hypoxia-inducible transcription factors (HIFs). The hypoxia-sensing mechanism involves oxygen limited hydroxylation of prolyl residues in the N- and C-terminal oxygen-dependent degradation domains (NODD and CODD) of HIFα isoforms, as catalysed by prolyl hydroxylases (PHD 1-3). Prolyl hydroxylation promotes binding of HIFα to the von Hippel-Lindau protein (VHL)-elongin B/C complex, thus signalling for proteosomal degradation of HIFα. We reveal that certain PHD2 variants linked to familial erythrocytosis and cancer are highly selective for CODD or NODD. Crystalline and solution state studies coupled to kinetic and cellular analyses reveal how wild-type and variant PHDs achieve ODD selectivity via different dynamic interactions involving loop and C-terminal regions. The results inform on how HIF target gene selectivity is achieved and will be of use in developing selective PHD inhibitors.


    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
    • 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.M.,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, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Egl nine homolog 1
A
252Homo sapiensMutation(s): 2 
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 5 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OGAKd: 2000 - 3400 nM (99) BINDINGDB
OGAKi: 8000 nM (99) BINDINGDB
OGAIC50: 5600 - 26000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 71.233α = 90.00
b = 71.233β = 90.00
c = 48.245γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2017-11-29
    Type: Database references