Structure of IDP90163
Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Reaction Intermediate.
- CSGID target
- IDP90163
- PDB Id
- 3JS3 (NCBI MMDB)
- Authors
- G.Minasov,S.H.Light,L.Shuvalova,I.Dubrovska,J.Winsor,S.N.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid)
- Responsible person
- George Minasov
- Responsible lab
- Northwestern University
- Deposition Date
- Sep 09, 2009
- Release Date
- Sep 22, 2009
Annotation
- Description
- The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven metabolic steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, the precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in animals.The dehydration of dehydroquinate to dehydroshikimate is an essential step in the shikimate pathway and is thus an attractive target for the development of novel antibiotics. In the pharmaceutical industry, shikimic acid from the Chinese star anise is used as a base material for production of Tamiflu (oseltamivir). Two distinct types of dehydroquinate dehydratases have been shown to catalyze the dehydration of dehydroquinate through disparate mechanisms. The protein we studied is representative of the type I enzyme, which is known to form Schiff base with the reaction intermediate. It has a typical TIM barrel fold with eight parallel beta strands, and active site located at the C-terminal ends of strands. The protein was co-crystallized with the 3-dehydroshikimate, which was found covalently bound to the highly conserved lysine in the active site. The reported structure represents the intermediate step in the dehydration of dehydroquinate to dehydroshikimate.
- Functional assignment
- 3-dehydroquinate dehydratase
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Ligands
| Ligand code | Name | Ligand type |
|---|---|---|
| DHS | 3-amino-4,5-dihydroxy-cyclohex-1-enecarboxylate | biological |
Structure information
Unit cell parameters
- Space Group
- P 1 21 1
- Unit Cell
-
a=60.47Å, b=139.62Å, c=66.77Å
α=90.00, β=90.63, γ=90.00 - Solvent content
- 49.05
- Matthews coefficient
- 2.41
- Resolution range
- 29.55-2.20Å (2.26-2.20Å)
- Rall(%)
- 19.2
- Rwork(%)
- 18.9 (28.0)
- Rfree(%)
- 24.1 (33.0)
- Num. observed reflections
- 55907 (4028)
- Num. Rfree reflections
- 2851 (214)
- Completeness(%)
- 99.8 (98.0)
- Num Atoms
- 8116
- Num Waters
- 318
- Num Hetatoms
- 366
- Model mean isotropic B factor (Å2)
- 21.950
- RMSD bond length (Å)
- 0.012
- RMSD bond angle
- 1.537°
- Filename uploaded
- rcsb055088.pdb (uploaded on Sep 11, 2009 7:25 PM)
- Inserted
- Sep 11, 2009
