Structure of IDP90626
1.90 Angstrom resolution crystal structure of N-terminal domain 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae
Edit deposit information
- CSGID target
- IDP90626
- PDB Id
- 3TI2 (NCBI MMDB)
- Authors
- S.H.Light,G.Minasov,A.S.Halavaty,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
- Aug 19, 2011
- Release Date
- Aug 31, 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. While the crystallization experiment began with intact, full-length protein electron density is only observed for the N-terminal domain. Based on an analysis of the crystal lattice, it is clear that there is not sufficient room for a disordered C-terminal domain and therefore we assume that the C-terminal domain was cleaved by contaminant protease present in the crystallization experiment. This structure represents an unliganded state of the enzyme. Consequently compared to the substrate-inhibitor complex (PDB code 3NVS), several active site loops are observed to adopt alternative conformations.
- Functional assignment
Ligands
| Ligand code | Name | Ligand type |
|---|---|---|
| PG4 | 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=77.76Å, b=40.07Å, c=133.86Å
α=90.00, β=90.33, γ=90.00 - Solvent content
- Matthews coefficient
- Resolution range
- 29.81-1.90Å (1.95-1.90Å)
- Rall(%)
- 15.3
- Rwork(%)
- 15.1 (22.5)
- Rfree(%)
- 19.6 (29.3)
- Num. observed reflections
- 65561 (4346)
- Num. Rfree reflections
- 3343 (228)
- Completeness(%)
- 99.6 (95.8)
- Num Atoms
- 7018
- Num Waters
- 676
- Num Hetatoms
- 719
- Model mean isotropic B factor
- 20.040Å2
- RMSD bond length
- 0.019Å
- RMSD bond angle
- 1.943°
- Filename uploaded
- rcsb067503.pdb (uploaded on Aug 23, 2011 3:55 PM)
- Inserted
- Aug 23, 2011