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Structure of IDP90922

Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in CovalentComplex with Dehydroquinate.

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CSGID target
IDP90922 
PDB Id
3M7W (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
Mar 17, 2010 
Release Date
Apr 07, 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. pH 4.6 crystals soaked with substrate, 3-dehydroquinic acid, produced a structure in which a covalently bound reaction intermediate is observed at the active site. Three residues (serine-232 through proline-235) which are disordered in the unliganded structure are visible in the ligand bound structure and interact with the reaction intermediate. Electron density corresponding to the leaving group is clearly visible and thus this structure represents a pre-dehydration intermediate state of the reaction. A comparison of this structure with the apo structure (PDB code: 3L2I) reveals a 1.5 Å movement of histidine-143, placing the residue within hydrogen bond distance from the leaving hydroxyl group. While the nature of the proton abstracting residue has been controversial (Leech et al., 1998), the direct interaction of histidine-143 with the leaving group positions the residue for proton shuttling between ring and leaving hydroxyl, a mechanism consistent with previous kinetic studies of the enzyme.  
Functional assignment
 

Ligands

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

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=184.33Å, b=66.58Å, c=128.23Å
α=90.00, β=119.08, γ=90.00 
Solvent content
40.69  
Matthews coefficient
2.07  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.69-1.95Å (2.00-1.95Å)  
Rall(%)
15.7 
Rwork(%)
15.4 (20.1) 
Rfree(%)
20.6 (27.4) 
Num. observed reflections
99109 (7189) 
Num. Rfree reflections
4955 (370) 
Completeness(%)
99.9 (99.1) 

Model parameters

Num Atoms
11646  
Num Waters
1108  
Num Hetatoms
1284  
Model mean isotropic B factor
20.010Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.447°  
Filename uploaded
rcsb058219.pdb (uploaded on Mar 30, 2010 6:42 PM)  
Inserted
Mar 30, 2010