5JZU

Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and factor X substrate peptide fragment (26mer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1038/s41467-019-12711-7
  • Primary Citation of Related Structures:  

  • 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 epid ...

    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.


    Organizational Affiliation

    NDORMS, Botnar Research Centre, University of Oxford, Old Road, Oxford, OX3 7LD, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK. christopher.schofield@chem.ox.ac.uk.,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.,Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartyl/asparaginyl beta-hydroxylase
A
429Homo sapiensMutation(s): 0 
Gene Names: ASPH (BAH)
EC: 1.14.11.16
Find proteins for Q12797 (Homo sapiens)
Go to Gene View: ASPH
Go to UniProtKB:  Q12797
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
B
26Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.230α = 90.00
b = 90.810β = 90.00
c = 124.090γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
PHASERphasing
xia2data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2019-11-06
    Type: Data collection, Database references