Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 169.46 kDa 
• Atom Count: 11231 
• Modelled Residue Count: 1340 
• Deposited Residue Count: 1456 
• Unique protein chains: 1

3LU1

Crystal Structure Analysis of WbgU: a UDP-GalNAc 4-epimerase

• PDB DOI: 10.2210/pdb3LU1/pdb

• Classification: ISOMERASE
• Organism(s): Plesiomonas shigelloides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-16 Released: 2010-07-21 
• Deposition Author(s): Bhatt, V.S., Guo, C.Y., Zhao, G., Yi, W., Liu, Z.J., Wang, P.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 

Literature

Altered architecture of substrate binding region defines the unique specificity of UDP-GalNAc 4-epimerases.

Bhatt, V.S., Guo, C.Y., Guan, W., Zhao, G., Yi, W., Liu, Z.J., Wang, P.G.

(2011) Protein Sci 20: 856-866

• PubMed: 21384454 
• DOI: 10.1002/pro.611
• Primary Citation of Related Structures:  
  3LU1


• PubMed Abstract: 
  

UDP-hexose 4-epimerases play a pivotal role in lipopolysaccharide (LPS) biosynthesis and Leloir pathway. These epimerases are classified into three groups based on whether they recognize nonacetylated UDP-hexoses (Group 1), both N-acetylated and nonacetylated UDP-hexoses (Group 2) or only N-acetylated UDP-hexoses (Group 3). Although the catalysis has been investigated extensively, yet a definitive model rationalizing the substrate specificity of all the three groups on a common platform is largely lacking. In this work, we present the crystal structure of WbgU, a novel UDP-hexose 4-epimerase that belongs to the Group 3. WbgU is involved in biosynthetic pathway of the unusual glycan 2-deoxy-L-altruronic acid that is found in the LPS of the pathogen Pleisomonas shigelloides. A model that defines its substrate specificity is proposed on the basis of the active site architecture. Representatives from all the three groups are then compared to rationalize their substrate specificity. This investigation reveals that the Group 3 active site architecture is markedly different from the "conserved scaffold" of the Group 1 and the Group 2 epimerases and highlights the interactions potentially responsible for the origin of specificity of the Group 3 epimerases toward N-acetylated hexoses. This study provides a platform for further engineering of the UDP-hexose 4-epimerases, leads to a deeper understanding of the LPS biosynthesis and carbohydrate recognition by proteins. It may also have implications in development of novel antibiotics and more economic synthesis of UDP-GalNAc and downstream products such as carbohydrate based vaccines.

---

Organizational Affiliation: 

Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WbgU	A, B, C, D	364	Plesiomonas shigelloides	Mutation(s): 0  Gene Names: wbgU EC: 5.1.3.7
UniProt
Find proteins for Q7BJX9 (Plesiomonas shigelloides) Explore Q7BJX9  Go to UniProtKB:  Q7BJX9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B], K [auth C], O [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UD2	F [auth A], I [auth B], L [auth C], P [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-NESSUJCYSA-N
SO4	M [auth C], R [auth D], S [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GLY	G [auth A], J [auth B], N [auth C], T [auth D]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
NA	Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.13	α = 90
b = 78.13	β = 90
c = 231.924	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-16 
• Released Date: 2010-07-21 
Deposition Author(s): Bhatt, V.S., Guo, C.Y., Zhao, G., Yi, W., Liu, Z.J., Wang, P.G.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-11-12
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description