prolyl hydroxylase from Trichoplax adhaerens

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.122 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Born to sense: biophysical analyses of the oxygen sensing prolyl hydroxylase from the simplest animal Trichoplax adhaerens.

Lippl, K.Boleininger, A.McDonough, M.A.Abboud, M.I.Tarhonskaya, H.Chowdhury, R.Loenarz, C.Schofield, C.J.

(2018) Hypoxia (Auckl) 6: 57-71

  • DOI: https://doi.org/10.2147/HP.S174655
  • Primary Citation of Related Structures:  
    6EY1, 6F0W

  • PubMed Abstract: 

    In humans and other animals, the chronic hypoxic response is mediated by hypoxia inducible transcription factors (HIFs) which regulate the expression of genes that counteract the effects of limiting oxygen. Prolyl hydroxylases (PHDs) act as hypoxia sensors for the HIF system in organisms ranging from humans to the simplest animal Trichoplax adhaerens . We report structural and biochemical studies on the T. adhaerens HIF prolyl hydroxylase ( Ta PHD) that inform about the evolution of hypoxia sensing in animals. High resolution crystal structures (≤1.3 Å) of Ta PHD, with and without its HIFα substrate, reveal remarkable conservation of key active site elements between T. adhaerens and human PHDs, which also manifest in kinetic comparisons. Conserved structural features of Ta PHD and human PHDs include those apparently enabling the slow binding/reaction of oxygen with the active site Fe(II), the formation of a stable 2-oxoglutarate complex, and a stereoelectronically promoted change in conformation of the hydroxylated proline-residue. Comparison of substrate selectivity between the human PHDs and Ta PHD provides insights into the selectivity determinants of HIF binding by the PHDs, and into the evolution of the multiple HIFs and PHDs present in higher animals.

  • Organizational Affiliation

    Chemistry Research Laboratory, University of Oxford, Oxford, UK, christopher.schofield@chem.ox.ac.uk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIF prolyl hydroxylase257Trichoplax adhaerensMutation(s): 0 
Gene Names: PHD
Find proteins for I6QVT6 (Trichoplax adhaerens)
Explore I6QVT6 
Go to UniProtKB:  I6QVT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6QVT6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.122 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.579α = 90
b = 59.413β = 100.74
c = 51.202γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description