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Structure of IDP90792

2.49 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate

Edit deposit information
CSGID target
IDP90792 
PDB Id
3PGJ (NCBI MMDB
Authors
A.S.Halavaty,S.H.Light,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Nov 02, 2010 
Release Date
Nov 24, 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. Shikimate dehydrogenase is an NADPH-dependent monomeric enzyme, which catalyzes the conversion of dehydroshikimate to shikimate, the fourth step in the shikimate pathway. This structure reveals that the N-terminal domain dehydroshikimate-binding domain has an alternating β-strand/α-helix character, whereas the C-terminal NADPH binding domain adopts a classical Rossman fold. In the asymmetric unit, four molecules forms two dimmers with the buried surface area of ~1800 A2. There is a single S-S bridge at the dimerization interface. The Rossmann fold domain is not involved in oligomerization. Each of the four molecules of the shikimate dehydrogenase has non-covalently associated shikimate. Binding of the ligand did not lead to big structural changes in the protein. Pairwise structural alignment of the apo-form and the binary complex structures reveals ~1.0 A r.m.s.d in the positions of the Cα atoms.  
Functional assignment
Oxidoreductase 

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 21 1  
Unit Cell

a=75.53Å, b=83.66Å, c=79.58Å
α=90.00, β=93.51, γ=90.00 
Solvent content
35.25  
Matthews coefficient
1.9  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.80-2.49Å (2.56-2.49Å)  
Rall(%)
19.6 
Rwork(%)
19.3 (25.6) 
Rfree(%)
24.7 (29.2) 
Num. observed reflections
34278 (2109) 
Num. Rfree reflections
1713 (118) 
Completeness(%)
98.7 (82.6) 

Model parameters

Num Atoms
8278  
Num Waters
115  
Num Hetatoms
163  
Model mean isotropic B factor
59.660Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.416°  
Filename uploaded
3PGJ.pdb (uploaded on Sep 28, 2011 11:13 AM)  
Inserted
Nov 02, 2010