Structure of IDP91169

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

Edit deposit information
CSGID target
IDP91169 
PDB Id
3TNL (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 01, 2011 
Release Date
Sep 28, 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, to which the reaction product, shikimate (added to the crystallization mixture), is observed to bind. The C-terminal domain adopts a classical Rossman fold, to which NAD (brought from the cell lysate) is observed to bind. The relative position of the two domains appears to be dynamic. All four molecules within the asymmetric unit are more closed than they are in the NAD bound structure but while two molecules are completely closed the other two adopt a conformation intermediate to the fully closed NAD + SHK structure and the open NAD structure.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
NAD biological
SKM 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=71.85Å, b=82.88Å, c=101.26Å
α=90.00, β=90.03, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.31-1.45Å (1.49-1.45Å)  
Rall(%)
15.0 
Rwork(%)
14.9 (23.7) 
Rfree(%)
17.6 (25.9) 
Num. observed reflections
202836 (13913) 
Num. Rfree reflections
10141 (673) 
Completeness(%)
96.7 (90.3) 

Model parameters

Num Atoms
9396  
Num Waters
1907  
Num Hetatoms
2218  
Model mean isotropic B factor
15.510Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.607°  
Filename uploaded
rcsb067692.pdb (uploaded on Sep 22, 2011 1:07 PM)  
Inserted
Sep 22, 2011