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Structure of IDP01842

1.70 Angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA) from Coxiella burnetii in complex with shikimate-3-phosphate and glyphosate

Edit deposit information
CSGID target
IDP01842 
PDB Id
3SLH (NCBI MMDB
Authors
S.H.Light,G.Minasov,E.V.Filippova,S.N.Krishna,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Sam Light 
Responsible lab
Northwestern University 
Deposition Date
Jun 24, 2011 
Release Date
Jul 20, 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. 3-phosphoshikimate 1- carboxyvinyltransferase is the sixth enzyme in the shikimate pathway and catalyzes the conversion of shikimate-3-phosphate and phosphoenolpyruvate to 5-enolpyruvyl-3-shikimate phosphate. This protein was co-crystallized with the substrate shikimate-3-phosphate and the commercially successful herbicide glyphosate. The enzyme consists of six βαβαββ motifs, three in both N- and C-terminal domains. Compared to the unliganded structure (PDB code 3ROI) the two domains adopt a closed conformation, at the interface of which the ligands are observed. Glyphosate binds adjacent to shikimate-3-phosphate in phosphoenolpyruvate’s binding site. Interestingly, two C-terminal apo state helices have partially unwound to present negatively charged residues at the active site.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
PEG crystallization
SKM biological
S3P shikimate-3-phosphate biological
GPJ glyphosate biological
CL CHLORIDE ION crystallization
BME crystallization
EDO crystallization
PO4 PHOSPHATE ION crystallization
1PE crystallization
PGE crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=46.25Å, b=186.64Å, c=95.79Å
α=90.00, β=91.51, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.64-1.70Å (1.74-1.70Å)  
Rall(%)
14.6 
Rwork(%)
14.4 (20.9) 
Rfree(%)
17.5 (23.2) 
Num. observed reflections
176839 (12694) 
Num. Rfree reflections
8841 (621) 
Completeness(%)
99.8 (97.4) 

Model parameters

Num Atoms
13426  
Num Waters
1525  
Num Hetatoms
1940  
Model mean isotropic B factor
23.590Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.525°  
Filename uploaded
rcsb066349.pdb (uploaded on Jul 01, 2011 7:53 PM)  
Inserted
Jul 01, 2011