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. A comparison of apo and reaction intermediate bound structures (PDB codes 3L2I and 3M7W) reveals a surface loop which is observed to close over the active upon substrate binding. The loop residue glutamine-236 is highly and conserved across species, implying that the residue may be functionally significant. To address the function of the loop we mutated glutamine-236 to alanine. The glutamine-236 to alanine mutant has profoundly deficient kinetics. This crystal structure reveals that loop closure in the mutant enzyme fails to relocate the residue arginine-214 – which is important in binding the substrate’s carboxylate - to its observed substrate binding position. Thus, this structure provides insight into the role of the loop and glutamine-236 in protein function.  

Functional assignment

dehydroquinate dehydratase 

Structure information

Unit cell parameters

Space Group

P 1  

Unit Cell

a=45.43Å, b=46.48Å, c=55.79Å
α=104.23, β=97.50, γ=98.70 

Solvent content

33.49  

Matthews coefficient

1.85  

Refinement

Data for the highest resolution shell is in parentheses.

Resolution range

26.62-1.03Å (1.06-1.03Å)  

R_all(%)

14.1 

R_work(%)

14.0 (17.5) 

R_free(%)

16.2 (18.5) 

Num. observed reflections

196962 (13252) 

Num. R_free reflections

9848 (666) 

Completeness(%)

92.6 (84.5) 

Model parameters

Num Atoms

4097  

Num Waters

775  

Num Hetatoms

854  

Model mean isotropic B factor

10.930Ų  

RMSD bond length

0.012Å  

RMSD bond angle

1.464°  

Filename uploaded

rcsb060551.pdb (uploaded on Aug 16, 2010 3:53 PM)  

Inserted

Aug 16, 2010