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Structure of IDP90922

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica typhimurium LT2 with Malonate and Boric Acid at the Active Site

Edit deposit information
CSGID target
S.H.Light,G.Minasov,M.-E.Duban,A.S.Halavaty,S.N.Krishna,L.Shuvalova,K.Kwon,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Sam Light 
Responsible lab
Northwestern University 
Deposition Date
May 18, 2011 
Release Date
Jun 01, 2011 


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. In this structure malonate and boric acid, components of the crystallization mixture, are observed within the active site of the enzyme. The two compounds are adjacently positioned and are in close enough proximity to form a hydrogen bonding interaction between oxygen atoms of malonate’s carboxyl group and boric acid’s hydroxyl group. A superposition with the substrate bound structure (PDB code 3M7W) reveals that the malonate mimics interactions made by the substrate’s carboxyl group, while the boric acid mimics interactions made by the substrate’s 4- and 5-hydroxyl groups. Similar to the enzyme-citrate complex (PDB code 3LB0), a surface loop that adopts an open and partially disordered in the enzyme’s apo-state (PDB 3L2I) but closes to form critical interactions with the substrate in the substrate bound-state, is observed to adopt a nearly closed conformation, which allows for the establishment of a loop-malonate hydrogen bond. Another interesting feature of this structure concerns the unusual behavior of the hexa-histidine purification tag. Within chain B the tag is partially ordered and two of its histidines, along with His134 from the protein, His134 from a chain A crystal contact, and an imadizole from the crystallization mixture are observed to coordinate a nickel ion.  
Functional assignment


Ligand code Name Ligand type
DMS dimethyl sulfoxide crystallization
MLA malonic acid biological
IMD crystallization
NI crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=36.56Å, b=72.57Å, c=171.35Å
α=90.00, β=90.00, γ=90.00 
Solvent content
Matthews coefficient


Data for the highest resolution shell is in parentheses.
Resolution range
28.56-1.45Å (1.49-1.45Å)  
14.4 (17.9) 
17.5 (20.1) 
Num. observed reflections
81695 (5688) 
Num. Rfree reflections
4084 (289) 
99.6 (96.0) 

Model parameters

Num Atoms
Num Waters
Num Hetatoms
Model mean isotropic B factor
RMSD bond length
RMSD bond angle
Filename uploaded
rcsb065734.pdb (uploaded on May 23, 2011 5:41 PM)  
May 23, 2011