Crystal Structure of WaaG, a glycosyltransferase involved in lipopolysaccharide biosynthesis

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Insights Into the Synthesis of Lipopolysaccharide and Antibiotics Through the Structures of Two Retaining Glycosyltransferases from Family Gt4

Martinez-Fleites, C.Proctor, M.Roberts, S.Bolam, D.N.Gilbert, H.J.Davies, G.J.

(2006) Chem Biol 13: 1143

  • DOI: https://doi.org/10.1016/j.chembiol.2006.09.005
  • Primary Citation of Related Structures:  
    2IUY, 2IV3, 2IV7, 2IW1

  • PubMed Abstract: 

    Glycosyltransferases (GTs) catalyze the synthesis of the myriad glycoconjugates that are central to life. One of the largest families is GT4, which contains several enzymes of therapeutic significance, exemplified by WaaG and AviGT4. WaaG catalyses a key step in lipopolysaccharide synthesis, while AviGT4, produced by Streptomyces viridochromogenes, contributes to the synthesis of the antibiotic avilamycin A. Here we present the crystal structure of both WaaG and AviGT4. The two enzymes contain two "Rossmann-like" (beta/alpha/beta) domains characteristic of the GT-B fold. Both recognition of the donor substrate and the catalytic machinery is similar to other retaining GTs that display the GT-B fold. Structural information is discussed with respect to the evolution of GTs and the therapeutic significance of the two enzymes.

  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN RFAG374Escherichia coli str. K-12 substr. W3110Mutation(s): 0 
Membrane Entity: Yes 
Find proteins for P25740 (Escherichia coli (strain K12))
Explore P25740 
Go to UniProtKB:  P25740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25740
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on U2F

Download Ideal Coordinates CCD File 
C15 H23 F N2 O16 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.718α = 90
b = 88.352β = 90
c = 89.342γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other