Crystal Structure of alpha1,3-Fucosyltransferase with GDP-fucose

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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Structure and mechanism of Helicobacter pylori fucosyltransferase. A basis for lipopolysaccharide variation and inhibitor design.

Sun, H.Y.Lin, S.W.Ko, T.P.Pan, J.F.Liu, C.L.Lin, C.N.Wang, A.H.Lin, C.H.

(2007) J Biol Chem 282: 9973-9982

  • DOI: https://doi.org/10.1074/jbc.M610285200
  • Primary Citation of Related Structures:  
    2NZW, 2NZX, 2NZY

  • PubMed Abstract: 

    Helicobacter pylori alpha1,3-fucosyltransferase (FucT) is involved in catalysis to produce the Lewis x trisaccharide, the major component of the bacteria's lipopolysaccharides, which has been suggested to mimic the surface sugars in gastric epithelium to escape host immune surveillance. We report here three x-ray crystal structures of FucT, including the FucT.GDP-fucose and FucT.GDP complexes. The protein structure is typical of the glycosyltransferase-B family despite little sequence homology. We identified a number of catalytically important residues, including Glu-95, which serves as the general base, and Glu-249, which stabilizes the developing oxonium ion during catalysis. The residues Arg-195, Tyr-246, Glu-249, and Lys-250 serve to interact with the donor substrate, GDP-fucose. Variations in the protein and ligand conformations, as well as a possible FucT dimer, were also observed. We propose a catalytic mechanism and a model of polysaccharide binding not only to explain the observed variations in H. pylori lipopolysaccharides, but also to facilitate the development of potent inhibitors.

  • Organizational Affiliation

    Institute of Biochemical Sciences, National Taiwan University, Taipei 10642; Institute of Biological Chemistry, Academia Sinica, No.128 Academia Road Section 2, Nan-Kang, Taipei 11529, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
371Helicobacter pyloriMutation(s): 0 
Gene Names: AF008596
Find proteins for O30511 (Helicobacter pylori)
Explore O30511 
Go to UniProtKB:  O30511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO30511
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]
C10 H15 N5 O11 P2
Query on FUC

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D [auth A],
F [auth B],
I [auth C]
C6 H12 O5
Query on SO4

Download Ideal Coordinates CCD File 
G [auth B],
J [auth C]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.962α = 90
b = 135.74β = 90
c = 96.19γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary