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Structure of IDP00152

2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acetylglucosamine 2-epimerase from Vibrio cholerae

Edit deposit information
CSGID target
IDP00152 
PDB Id
3DZC (NCBI MMDB
Authors
G.Minasov,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,K.Kwon,J.Hasseman,S.N.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jul 29, 2008 
Release Date
Aug 12, 2008 

Annotation

Description
An UDP-N-acetylglucosamine 2-epimerase belongs to the family of isomerase, specifically those racemases and epimarases which act on carbohydrates and participate in amino sugars metabolism. Amino sugars are parts of aminoglycosides, a class of antimicrobial compounds that inhibit bacterial protein synthesis. The Enzyme catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) to produce UDP-N-acetylmannosamine (UDP-ManNAc). The presented crystal structure is an apo-form of the protein. The homodimeric epimerase is composed of two similar alpha/beta/alpha sandwich domains with the active site located in the deep cleft at the domain interface. Comparison with other known structures (apo- and complexes with substrate) has revealed big interdomain movement that is implicated in the regulatory mechanism. 
Functional assignment
UDP-N-acetylglucosamine 2-epimerase 

Ligands

Ligand code Name Ligand type
CL
CA

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=81.39Å, b=88.13Å, c=132.19Å
α=90.00, β=90.00, γ=90.00 
Solvent content
54.52  
Matthews coefficient
2.7  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.00-2.35Å (2.41-2.35Å)  
Rall(%)
17.5 
Rwork(%)
17.2 (19.4) 
Rfree(%)
23.4 (26.9) 
Num. observed reflections
40275 (2921) 
Num. Rfree reflections
2013 (135) 
Completeness(%)
99.9 (99.5) 

Model parameters

Num Atoms
6112  
Num Waters
488  
Num Hetatoms
504  
Model mean isotropic B factor
43.450Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.612°  
Filename uploaded
3dzc.pdb (uploaded on Oct 27, 2008 1:45 PM)  
Inserted
Oct 27, 2008