6EY1

prolyl hydroxylase from Trichoplax adhaerens

• PDB DOI: https://doi.org/10.2210/pdb6EY1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trichoplax adhaerens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-11-10 Released: 2018-10-03 
• Deposition Author(s): McDonough, M.A., Boleininger, A.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.138 
• R-Value Work: 0.122 
• R-Value Observed: 0.122 

Literature

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

• PubMed: 30519597 
• 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 .

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Organizational Affiliation: 

Chemistry Research Laboratory, University of Oxford, Oxford, UK, [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.54 kDa 
• Atom Count: 2,026 
• Modelled Residue Count: 211 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIF prolyl hydroxylase	A	257	Trichoplax adhaerens	Mutation(s): 0  Gene Names: PHD
UniProt
Find proteins for I6QVT6 (Trichoplax adhaerens) Explore I6QVT6  Go to UniProtKB:  I6QVT6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B [auth A], C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 40.579	α = 90
b = 59.413	β = 100.74
c = 51.202	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): McDonough, M.A., Boleininger, A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History  

• 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