Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 101.22 
• Atom Count: 7223 
• Residue Count: 875 
• Unique protein chains: 2

6RK9

Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and cyclic peptide substrate mimic of factor X

• DOI: 10.2210/pdb6RK9/pdb
• Entry: 6RK9 supersedes: 5JZZ

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG


• Deposited: 2019-04-30 Released: 2019-05-08 
• Deposition Author(s): McDonough, M.A., Pfeffer, I.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.235 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

• 5JZZ

Literature

Aspartate/asparagine-beta-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern.

Pfeffer, I., Brewitz, L., Krojer, T., Jensen, S.A., Kochan, G.T., Kershaw, N.J., Hewitson, K.S., McNeill, L.A., Kramer, H., Munzel, M., Hopkinson, R.J., Oppermann, U., Handford, P.A., McDonough, M.A., Schofield, C.J.

(2019) Nat Commun 10: 4910-4910

• PubMed: 31659163 
• DOI: 10.1038/s41467-019-12711-7
• Structures With Same Primary Citation


• PubMed Abstract: 
  

AspH is an endoplasmic reticulum (ER) membrane-anchored 2-oxoglutarate oxygenase whose C-terminal oxygenase and tetratricopeptide repeat (TPR) domains present in the ER lumen. AspH catalyses hydroxylation of asparaginyl- and aspartyl-residues in epidermal growth factor-like domains (EGFDs). Here we report crystal structures of human AspH, with and without substrate, that reveal substantial conformational changes of the oxygenase and TPR domains during substrate binding. Fe(II)-binding by AspH is unusual, employing only two Fe(II)-binding ligands (His679/His725). Most EGFD structures adopt an established fold with a conserved Cys1-3, 2-4, 5-6 disulfide bonding pattern; an unexpected Cys3-4 disulfide bonding pattern is observed in AspH-EGFD substrate complexes, the catalytic relevance of which is supported by studies involving stable cyclic peptide substrate analogues and by effects of Ca(II) ions on activity. The results have implications for EGFD disulfide pattern processing in the ER and will enable medicinal chemistry efforts targeting human 2OG oxygenases.

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Organizational Affiliation: 

Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aspartyl/asparaginyl beta-hydroxylase	A, B	429	Homo sapiens	Mutation(s): 0  Gene Names: ASPH, BAH EC: 1.14.11.16
Find proteins for Q12797 (Homo sapiens) Go to UniProtKB:  Q12797
NIH Common Fund Data Resources
PHAROS  Q12797 GTEx  ENSG00000198363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ACA-LYS-ASP-GLY-LEU-GLY-GLU-TYR-THR-CYS-THR-SER-LEU-GLU-GLY-PHE-GLU	C	19	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.235 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.472	α = 103.97
b = 59.243	β = 91.49
c = 95.665	γ = 92.7

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-30 
• Released Date: 2019-05-08 
Deposition Author(s): McDonough, M.A., Pfeffer, I.
• This entry supersedes: 5JZZ

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History 

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references