5L9B

HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-1ALPHA CODD (556-574)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 
    • 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
    • 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


    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, B
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hypoxia-inducible factor 1-alpha
C, D
19Homo sapiensMutation(s): 0 
Gene Names: HIF1A (BHLHE78, MOP1, PASD8)
Find proteins for Q16665 (Homo sapiens)
Go to Gene View: HIF1A
Go to UniProtKB:  Q16665
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A, B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.193α = 90.00
b = 76.395β = 90.03
c = 70.962γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

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