9SP7 | pdb_00009sp7

Human galactosyltransferase B3GalT6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.202 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Human Proteoglycan Linkage Region Glycosyltransferases are Dimeric and Show Unexpected Specificities.

Weidler, S.Bundgaard, O.Hessefort, M.Radisch, M.Graf, C.G.F.Lam, K.Neubauer, V.J.Eisenreich, J.Kohler, L.Moremen, K.W.Steentoft, C.Clausen, H.Huang, T.Y.Hung, S.C.Steegborn, C.Weyand, M.Unverzagt, C.

(2026) Angew Chem Int Ed Engl 65: e16855-e16855

  • DOI: https://doi.org/10.1002/anie.202516855
  • Primary Citation of Related Structures:  
    9SP7

  • PubMed Abstract: 

    We selected the N,O-glycosylated proteoglycan bikunin as a model to establish a chemoenzymatic approach to defined proteoglycans using native chemical ligation. Overexpression of the human linkage region glycosyltransferases B4GalT7, B3GalT6 and B3GlcAT-1 as N-terminal SUMO-fusions gave high yields of soluble and active enzymes in E. coli. When starting with xylosylated bikunin peptides the transferases performed well in enzymatic cascade reactions and provided the desired linkage region tetrasaccharide glycopeptides. B3GalT6 and B3GlcAT-1 led to side products with N,O-glycosylated bikunin peptides revealing unexpected promiscuity of both enzymes towards complex type N-glycans. Additionally, B3GalT6 was found to synthesize short poly-β3 Gal structures. B3GlcAT-1 can slowly convert the biosynthetic intermediate Gal-Xyl to the non-canonical trisaccharide GlcA-Gal-Xyl. This reaction independently confirmed the recently detected biosynthetic bypass to GAGs in the case of dysfunctional B3GalT6 (spondylodysplastic Ehlers-Danlos-syndrome). The three linkage region glycosyltransferases B4GalT7, B3GalT6 and B3GlcAT-1 were dimeric in solution and the crystal structure of B3GalT6 was solved showing a covalent dimer linked by a disulfide in the center of the large dimerization domain. This motif appears to be conserved in higher organisms and reinforces the concept of dimeric glycosyltransferases lining the Golgi.


  • Organizational Affiliation
    • University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-1,3-galactosyltransferase 6294Homo sapiensMutation(s): 0 
Gene Names: B3GALT6
EC: 2.4.1.134
UniProt & NIH Common Fund Data Resources
Find proteins for Q96L58 (Homo sapiens)
Explore Q96L58 
Go to UniProtKB:  Q96L58
PHAROS:  Q96L58
GTEx:  ENSG00000176022 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96L58
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.202 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.25α = 90
b = 77.46β = 90
c = 151.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySPP 1623
National Science Foundation (NSF, United States)United StatesNSF 2400220

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references