Team:British Columbia/Model3

Monoterpene Synthase Structural Modeling

Objective: To identify amino acid residues that are terpene synthesis, we constructed three-dimensional models of the terpene synthase proteins.

Model Creators: Joe Ho, Samuel Wu

Model Advisors: Shing Hei Zhan, Alina Chan

Three-dimensional Models of the 3 Terpene Synthases

Ribbon representation of the alpha-pinene synthase (HQ426166).

Ribbon representation of the beta-pinene synthase (HQ426154).

Ribbon representation of the limonene synthase ().

Superimposition of the 3D structures of the three synthase (blue), beta-pinene synthase (red), and limonene synthase (green).

Reactive site of the alpha-pinene synthase

Skin representation of the reactive site of alpha-pinene synthase. Geranyl diphosphate (GDP) is docked inside the pocket. The oxygen atoms (red spheres) belonging to the phosphate groups of GDP and the carbon atoms (yellow spheres) forming the backbone of GDP are shown.

Materials and Methods

We used MODELLER (1) to automate homology-based 3D structure prediction. We identified an experimentally determined 3D structure of a taxadiene synthase from Pacific Yew (PDB ID: 3P5R) as an appropriate template. The image was taken using the freely available ICM Browser.

Future Directions

References

1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.