Team:British Columbia/Model3

From 2011.igem.org

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<b>Model Advisors:</b> Shing Hei Zhan, Alina Chan <p></p>
<b>Model Advisors:</b> Shing Hei Zhan, Alina Chan <p></p>
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<html><h3>Three-dimensional structure of the 3 terpene synthases</h3></html><p></p>
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<html><h3>Three-dimensional Models of the 3 Terpene Synthases</h3></html><p></p>
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[[File:UBCiGEM superimposed synthases.jpg]]
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[[File:UBCiGEM aTP ribbon.jpg]]
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<p></p>Superimposition of the 3D structures of alpha-pinene synthase (blue), beta-pinene synthase (red), and limonene synthase (green). 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.<p></p>
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<b>Ribbon representation of the alpha-pinene synthase (HQ426166).</b><p></p>
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[[File:UBCiGEM bTP ribbon.jpg]]
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<b>Ribbon representation of the beta-pinene synthase (HQ426154).</b><p></p>
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[[File:UBCiGEM lTP ribbon.jpg]]
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<b>Ribbon representation of the limonene synthase ().</b><p></p>
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[[File:UBCiGEM superimposed ribbon.jpg]]
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<p></p>Superimposition of the 3D structures of the three synthase (blue), beta-pinene synthase (red), and limonene synthase (green).<p></p>
<b>Reactive site of the three synthases</b><p></p>
<b>Reactive site of the three synthases</b><p></p>
[[File:UBCiGEM model3 reactive site.jpg]]
[[File:UBCiGEM model3 reactive site.jpg]]
Magnesium ions are cofactors located at the reactive site.
Magnesium ions are cofactors located at the reactive site.
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<html><h3>Materials and Methods</h3></html><p></p>
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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.
<html><h3>Future Directions</h3></html><p></p>
<html><h3>Future Directions</h3></html><p></p>

Revision as of 03:14, 29 October 2011

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 Models of the 3 Terpene Synthases

UBCiGEM aTP ribbon.jpg

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

UBCiGEM bTP ribbon.jpg

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

UBCiGEM lTP ribbon.jpg

Ribbon representation of the limonene synthase ().

UBCiGEM superimposed ribbon.jpg

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

Reactive site of the three synthases

UBCiGEM model3 reactive site.jpg Magnesium ions are cofactors located at the reactive site.

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.

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