Structure of IDP91169

2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.

Edit deposit information
CSGID target
IDP91169 
PDB Id
3TOZ (NCBI MMDB
Authors
G.Minasov,S.H.Light,A.Halavaty,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
Sep 06, 2011 
Release Date
Sep 21, 2011 

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 NAD(P)H-dependent monomeric enzyme which catalyzes the conversion of dehydroshikimate to shikimate, the fourth step in the shikimate pathway. This structure has an N-terminal domain with an alternating β-strand/α-helix character. Whereas, the C-terminal domain adopts a classical Rossman fold, to which NAD (brought from the cell lysate) is observed to bind.  
Functional assignment
 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=70.13Å, b=78.43Å, c=214.83Å
α=90.00, β=90.49, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.63-2.20Å (2.26-2.20Å)  
Rall(%)
19.9 
Rwork(%)
19.5 (26.1) 
Rfree(%)
25.6 (32.5) 
Num. observed reflections
116413 (8398) 
Num. Rfree reflections
5820 (383) 
Completeness(%)
98.2 (97.3) 

Model parameters

Num Atoms
18177  
Num Waters
1010  
Num Hetatoms
1426  
Model mean isotropic B factor
33.410Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.568°  
Filename uploaded
rcsb067742.pdb (uploaded on Sep 22, 2011 12:51 PM)  
Inserted
Sep 22, 2011