Team:British Columbia/Model3

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Team: British Columbia - 2011.igem.org

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 Structure of the 3 Terpene Synthase Proteins

Ribbon representation of the alpha-pinene synthase.

Ribbon representation of the beta-pinene synthase.

Ribbon representation of the limonene synthase.

Superimposition of the 3D structures of the three synthase (blue), beta-pinene synthase (red), and limonene synthase (green). The synthases exhibit high structural similarity. This observation allows us to identify homologous amino acid residues that may affect terpene synthesis efficiency.

Reactive site of the alpha-pinene synthase

Skin representation of the reactive site of alpha-pinene synthase. The substrate, geranyl diphosphate (GDP), is docked inside the reactive 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. Magnesium ion cofactors (blue spheres) interact with GDP.

Alternative representation of the reactive site of alpha-pinene synthase. The synthase structure is shown in ribbon model and the substrate GDP in ball-and-stick model. The magnesium ion cofactors are represented by blue spheres. The dotted light blue lines indicate hydrogen bonds.

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. All images were taken using the ICM by Molsoft LLC (2).

Future Directions

The current study a

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. 2. Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.A. Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation. J. Comp. Chem. 15, 488-506. 1994.

Acknowledgment

We are very grateful to Yvonne Y. Li from the BC Genome Sciences Centre for valuable technical advice.

@@ Line 24: / Line 24: @@
 <html><h3>Reactive site of the alpha-pinene synthase</h3></html><p></p>
 [[File:UBCiGEM skin dock.jpg]]
-Skin representation of the reactive site of alpha-pinene synthase. The substrate, geranyl diphosphate (GDP), is docked inside the reactive 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. Magnesium ion cofactors (blue spheres) interact with GDP.<p></p>
+<p></p><b>Skin representation of the reactive site of alpha-pinene synthase. The substrate, geranyl diphosphate (GDP), is docked inside the reactive 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. Magnesium ion cofactors (blue spheres) interact with GDP.</b><p></p>
 [[File:UBCiGEM skeletal dock.jpg]]
-Alternative representation of the reactive site of alpha-pinene synthase. The synthase structure is shown in ribbon model and the substrate GDP in ball-and-stick model. The magnesium ion cofactors are represented by blue spheres. The dotted light blue lines indicate hydrogen bonds.<p></p>
+<p></p><b>Alternative representation of the reactive site of alpha-pinene synthase. The synthase structure is shown in ribbon model and the substrate GDP in ball-and-stick model. The magnesium ion cofactors are represented by blue spheres. The dotted light blue lines indicate hydrogen bonds.</b><p></p>
 <html><h3>Materials and Methods</h3></html><p></p>
-The HQ426166, HQ426154, AY473624. 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.
+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. All images were taken using the ICM by Molsoft LLC (2).
 <html><h3>Future Directions</h3></html><p></p>
+The current study a
 <html><h3>References</h3></html><p></p>
 . 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.
+. Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.A. Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation. J. Comp. Chem. 15, 488-506. 1994.
+<html><h3>Acknowledgment</h3></html><p></p>
+We are very grateful to Yvonne Y. Li from the BC Genome Sciences Centre for valuable technical advice.