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
- 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)
- 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