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Structure of IDP01656

2.2 Angstrom Resolution Crystal Structure of putative UDP-N-acetylglucosamine 2-epimerase from Listeria monocytogenes

Edit deposit information
CSGID target
IDP01656 
PDB Id
3OT5 (NCBI MMDB
Authors
G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Sep 10, 2010 
Release Date
Sep 22, 2010 

Annotation

Description
The non-hydrolysing bacterial UDP-N-acetylglucosamine 2-epimerase (UDP-GlcNAc 2-epimerase) catalyses the conversion of UDP-GlcNAc into UDP-N-acetylmannosamine, an intermediate in the biosynthesis of several cell-surface polysaccharides. This enzyme is allosterically regulated by its substrate UDP-GlcNAc. The crystal structure (PDB ID code 3OT5) of a putative UDP-N-acetylglucosamine 2-epimerase from Listeria monocytogenes has been solved and refined to 2.2 A resolution. The asymmetric unit contains four copies of the protein. The homologous B. anthracis (PDB ID code 3BEO) and L. monocytogenes UDP-GlcNAc 2-epimerases share 65 % sequence identity and have rmsd values from 2.0 to 4.0 A in the positions of their 361 C-alpha atoms, as revealed by the pairwise structural alignment. These big overall differences might be related to the conformational changes that take place in protein upon binding of the substrate UDP-GlcNAc and the reaction intermediate UDP in the 3BEO structure. Indeed, superposition of the B. anthracis apo-UDP-GlcNAc 2-epimerase structure (PDB ID code 1O6C) and the 3OT5 structure shows rmsd values from 1.2 to 2.9 A over the aforementioned range of the C-alpha atoms. Additionally, both apo-form structures exhibit a high overall mean B value of 49.0 A2, whereas it is 13.0 A2 in the ternary complex 3BEO structure.  
Functional assignment
Isomerase 

Ligands

Ligand code Name Ligand type
PEG polyethylene glycol
PGE TRIETHYLENE GLYCOL

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=81.19Å, b=84.41Å, c=100.46Å
α=90.00, β=90.07, γ=90.00 
Solvent content
35.6  
Matthews coefficient
1.91  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.59-2.20Å (2.26-2.20Å)  
Rall(%)
19.0 
Rwork(%)
18.7 (26.3) 
Rfree(%)
23.5 (34.2) 
Num. observed reflections
67545 (4056) 
Num. Rfree reflections
3444 (196) 
Completeness(%)
98.1 (80.3) 

Model parameters

Num Atoms
11742  
Num Waters
237  
Num Hetatoms
257  
Model mean isotropic B factor
47.290Å2  
RMSD bond length
0.009Å  
RMSD bond angle
1.378°  
Filename uploaded
rcsb061540.pdb (uploaded on Sep 17, 2010 5:33 PM)  
Inserted
Sep 17, 2010