3DOO

Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis complexed with shikimate

Summary for 3DOO

• Entry DOI: 10.2210/pdb3doo/pdb
• Related: 3DON
• Descriptor: Shikimate dehydrogenase, (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID (3 entities in total)
• Functional Keywords: alpha-beta structure, rossmann fold, amino-acid biosynthesis, aromatic amino acid biosynthesis, nadp, oxidoreductase
• Biological source: Staphylococcus epidermidis
• Total number of polymer chains: 1
• Total formula weight: 31224.43

Authors

Han, C.,Hu, T.,Wu, D.,Zhou, J.,Shen, X.,Qu, D.,Jiang, H. (deposition date: 2008-07-05, release date: 2009-05-05, Last modification date: 2023-11-01)

Primary citation

Han, C.,Hu, T.,Wu, D.,Qu, S.,Zhou, J.,Ding, J.,Shen, X.,Qu, D.,Jiang, H.
X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis
Febs J., 276:1125-1139, 2009

PubMed Abstract: Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. In this study, we determined the kinetic properties and crystal structures of Staphylococcus epidermidis SDH (SeSDH) both in its ligand-free form and in complex with shikimate. SeSDH has a k(cat) of 22.8 s(-1) and a K(m) of 73 mum towards shikimate, and a K(m) of 100 microM towards NADP. The overall folding of SeSDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211, normally regarded as important for substrate binding, does not interact with shikimate in the binary SeSDH-shikimate complex structure. However, the Y211F mutation leads to a significant decrease in k(cat) and a minor increase in the K(m) for shikimate. The results indicate that the main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SeSDH is less conserved. The usually long helix specifically recognizing the adenine ribose phosphate is substituted with a short 3(10) helix in the NADP-binding domain. Moreover, the interdomain angle of SeSDH is the widest among all known SDH structures, indicating an inactive 'open' state of the SeSDH structure. Thus, a 'closing' process might occur upon NADP binding to bring the cofactor close to the substrate for catalysis.

PubMed: 19215302
DOI: 10.1111/j.1742-4658.2008.06856.x

Experimental method

X-RAY DIFFRACTION (2.2 Å)