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Structure of IDP01254

2.76 Angstrom Crystal Structure of a Putative Glucose-1-Phosphate Thymidylyltransferase from Bacillus anthracis in Complex with a Sucrose.

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CSGID target
IDP01254 
PDB Id
3HL3 (NCBI MMDB) 
Authors
G.Minasov,L.Shuvalova,A.Halavaty,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
May 26, 2009 
Release Date
Jun 09, 2009 

Annotation

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Description
The biosynthetic pathway for the production of dTDP-L-rhamnose is composed of four enzymes. The first enzyme, glucose-1-phosphate thymidylyltransferase, is the control enzyme of the pathway and is capable of utilizing dTTP or UTP. This pathway is essential for production of the activated sugar dTDP-L-rhamnose for capsular polysaccharide synthesis in gram-positive bacteria, and it is absent in humans. Thus, this pathway is a good candidate for drug discovery efforts. Our structure is the first one of this enzyme in gram-positive bacteria, and it contains a sucrose molecule bound in the active site. 
Functional assignment
glucose-1-phosphate thymidylyltransferase 

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

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Unit cell parameters

Space Group
P 6 2 2  
Unit Cell

a=134.43Å, b=134.43Å, c=85.27Å
α=90.00, β=90.00, γ=120.00 
Solvent content
66.51  
Matthews coefficient
3.67  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.10-2.76Å (2.83-2.76Å)  
Rall(%)
17.5 
Rwork(%)
17.3 (24.8) 
Rfree(%)
20.6 (26.7) 
Num. observed reflections
12153 (851) 
Num. Rfree reflections
583 (44) 
Completeness(%)
99.8 (97.7) 

Model parameters

Num Atoms
1993  
Num Waters
37  
Num Hetatoms
60  
Model mean isotropic B factor
30.530Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.546°  
Filename uploaded
idp01254c.pdb (uploaded on May 26, 2009 6:50 PM)  
Inserted
May 26, 2009