2IV7 | pdb_00002iv7

Crystal Structure of WaaG, a glycosyltransferase involved in lipopolysaccharide biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb2IV7/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli str. K-12 substr. W3110
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-08 Released: 2006-10-11 
• Deposition Author(s): Martinez-Fleites, C., Proctor, M., Roberts, S., Bolam, D.N., Gilbert, H.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.201 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

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

• PubMed: 17113996 
• DOI: https://doi.org/10.1016/j.chembiol.2006.09.005
• Primary Citation 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.

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Organizational Affiliation: 
• York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 43.07 kDa 
• Atom Count: 3,502 
• Modeled Residue Count: 370 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN RFAG	A	374	Escherichia coli str. K-12 substr. W3110	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for P25740 (Escherichia coli (strain K12)) Explore P25740  Go to UniProtKB:  P25740

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	B [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.201 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.69	α = 90
b = 88.664	β = 90
c = 89.594	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-11 
Deposition Author(s): Martinez-Fleites, C., Proctor, M., Roberts, S., Bolam, D.N., Gilbert, H.J., Davies, G.J.

Revision History  

• 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: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary