8RE5 | pdb_00008re5

Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735Q variant in complex with Mn, 2-oxosuberate and a Factor X derived peptide fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.207 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and functional consequences of aspartate/asparagine-beta-hydroxylase variants causing Traboulsi Syndrome.

Hou, C.X.Brasnett, A.Rabe, P.Schofield, C.J.Brewitz, L.

(2025) J Biological Chem : 111008-111008

  • DOI: https://doi.org/10.1016/j.jbc.2025.111008
  • Primary Citation of Related Structures:  
    8RE5, 8RE6, 8RE7, 8RE8, 8RE9

  • PubMed Abstract: 

    Traboulsi Syndrome is an autosomal recessive hereditary disease associated with developmental defects, in particular of the ocular system. Single nucleotide polymorphisms affecting the ASPH gene, which encodes for the 2-oxoglutarate (2OG)-dependent oxygenase aspartate/asparagine-β-hydroxylase (AspH), are associated with Traboulsi Syndrome. AspH catalyzes hydroxylations of conserved aspartate/asparagine residues in epidermal growth factor-like domain (EGFD) proteins. We report studies on the clinically-observed Traboulsi Syndrome-associated R688Q, R735Q, and R735W AspH variants. The results reveal that pathogenic active site substitutions substantially reduce, though do not ablate, EGFD hydroxylase activity compared to wildtype AspH. They imply that efficient AspH catalyzed EGFD hydroxylation is important during human development. Crystallographic studies reveal conservation of the overall AspH fold, but that the preferred conformations of 2OG in complex with the R735Q and R735W AspH variants differ from that with wildtype AspH. Screening of potential 2OG cosubstrate substitutes reveals certain 2-oxoacids, including naturally present metabolites, manifest enhanced catalytic efficiency of Traboulsi Syndrome-associated AspH variants compared to 2OG. The results thus provide proof-of-principle for a therapeutic strategy involving rescue of impaired activities of pathogenic active site AspH variants by use of 2-oxoacids, or 2-oxoacid precursors, other than 2OG.


  • Organizational Affiliation
    • Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartyl/asparaginyl beta-hydroxylase444Homo sapiensMutation(s): 1 
Gene Names: ASPHBAH
EC: 1.14.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q12797 (Homo sapiens)
Explore Q12797 
Go to UniProtKB:  Q12797
PHAROS:  Q12797
GTEx:  ENSG00000198363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12797
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor X39synthetic constructMutation(s): 4 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.207 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.361α = 90
b = 86.343β = 90
c = 123.795γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106244/Z/14/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V001892/1
Wellcome TrustUnited Kingdom227298/Z/23/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references