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Structure of IDP90922

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Citrate Bound to the Active Site.

Edit deposit information
CSGID target
IDP90922 
PDB Id
3LB0 (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
Jan 07, 2010 
Release Date
Jan 26, 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 low pH crystal structure has the interesting feature of differential ligand occupancy in the biological dimer’s two active sites. In one active site a citrate from the crystallization condition is bound. A comparison of citrate with reaction intermediate binding shows that the citrate mimicks many of the interactions made by the intermediate. Citrate is not observed in the asymmetric unit’s other active site. Rather, a tris molecule, also from the crystallization condition, is observed. A noteworthy distinction between the differentially occupied active sites lies in the location of a mobile region spanning serine-232 to glutamine-236. In the tris bound molecule these residues have poor electron density and are therefore not modeled but in the citrate bound molecule they are visible and interact with the citrate molecule. The disordered behavior of this region is also observed in the apo structure (PDB code: 3L2I) while the ordered behavior is similar in the reaction intermediate bound structure (PDB code: 3M7W). Thus, the crystal structure presented here displays properties associated with both apo and intermediate bound structures. The basis of this active site non-equivalence is unknown but may result from constraints imposed by crystal packing.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
FMT crystallization
TRS Tris(hydroxymethyl)aminomethane crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=36.89Å, b=45.85Å, c=80.82Å
α=93.95, β=101.19, γ=105.49 
Solvent content
42.22  
Matthews coefficient
2.13  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
26.30-1.65Å (1.69-1.65Å)  
Rall(%)
16.2 
Rwork(%)
16.0 (18.3) 
Rfree(%)
20.1 (22.9) 
Num. observed reflections
56084 (4226) 
Num. Rfree reflections
2804 (188) 
Completeness(%)
93.9 (95.0) 

Model parameters

Num Atoms
4333  
Num Waters
587  
Num Hetatoms
624  
Model mean isotropic B factor
17.110Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.471°  
Filename uploaded
rcsb057055.pdb (uploaded on Jan 18, 2010 9:24 PM)  
Inserted
Jan 18, 2010