To see full content of that page you need the activeISee plugin.
Get the latest version from here.

Structure of IDP90922

Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Non-Covalent Complex with Dehydroquinate.

Edit deposit information
CSGID target
IDP90922 
PDB Id
3NNT (NCBI MMDB
Authors
G.Minasov,S.H.Light,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jun 24, 2010 
Release Date
Jul 28, 2010 

Annotation

Description
The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, a precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in humans, making it an attractive target for the development of novel antibiotics. The third step in the pathway consists of the dehydration of dehydroquinate to dehydroshikimate. This reaction can be catalyzed by two enzyme families which utilize distinct mechanisms. The protein structure presented here is representative of the type I enzyme family. This enzyme’s reaction mechanism is known to involve a covalent Schiff base intermediate. We previously obtained structures characterizing two covalent intermediate states of the enzyme (PDB codes: 3JS3 and 3M7W). To obtain insight in the substrate binding event, the Schiff base forming lysine-170 was mutated to methionine. Co-crystallization of this mutant protein with substrate, 3-dehydroquinic acid, produced this structure in which the substrate is observed non-covalently bound at the active site. The substrate’s ring core is similarly positioned within the active site compared to the covalent intermediates which demonstrates a similar mode of binding in the absence of covalent bond formation.  
Functional assignment
 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=36.73Å, b=43.55Å, c=79.94Å
α=91.18, β=101.27, γ=109.05 
Solvent content
37.26  
Matthews coefficient
1.96  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.65-1.60Å (1.64-1.60Å)  
Rall(%)
15.9 
Rwork(%)
15.8 (23.4) 
Rfree(%)
18.7 (26.3) 
Num. observed reflections
58355 (4193) 
Num. Rfree reflections
2976 (215) 
Completeness(%)
96.8 (95.2) 

Model parameters

Num Atoms
4151  
Num Waters
525  
Num Hetatoms
567  
Model mean isotropic B factor
19.540Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.409°  
Filename uploaded
rcsb060059.pdb (uploaded on Aug 02, 2010 7:32 PM)  
Inserted
Aug 02, 2010