6F0W

prolyl hydroxylase in complex with hypoxia inducible factor oxygen degradation domain peptide fragment from Trichoplax adhaerens

• PDB DOI: https://doi.org/10.2210/pdb6F0W/pdb

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


• Deposited: 2017-11-20 Released: 2018-10-03 
• Deposition Author(s): McDonough, M.A., Boleininger, A., Schofield, C.J.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.162 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 

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: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.9 kDa 
• Atom Count: 2,146 
• Modelled Residue Count: 238 
• Deposited Residue Count: 278 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxia inducible factor, alpha subunit	B [auth S]	21	Trichoplax adhaerens	Mutation(s): 0
UniProt
Find proteins for B3RXX2 (Trichoplax adhaerens) Explore B3RXX2  Go to UniProtKB:  B3RXX2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA	C [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.162 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.841	α = 114.06
b = 41.321	β = 95.67
c = 42.076	γ = 103.69

Software Package:

Software Name	Purpose
PHENIX	refinement
GDA	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
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., Schofield, C.J.

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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, Derived calculations, Refinement description