Sandbox Reserved 1692

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function of your protein

Our protein, L-rhamnose- α-1,4-D-glucuronate lyase (FoRham1), derived from the fungus Fusarium oxysporum, is a helpful tool for determining the structure and function of Gum Arabic (GA) to create potential agents to degrade GA more effectively. FoRham1, when bound to GA, will remove the Rha-caps from the nonreducing ends of GA. Enzymes that can react with glycosidic linkages of certain carbohydrates can be useful in determining the structure, function, and mechanism of the carbohydrates, giving scientists the tools to manipulate their physical properties for further application. Understanding the mechanism will give researchers more tools to understand how to degrade GA. Specifically, I focused on the mutant H105F, which has a PDB file of 7ESN. Here, I have the protein using N->C coloring.

Biological relevance and broader implications

Gum Arabic (GA) is a representative protein of the family of arabinogalactan proteins (AGPs) and is produced in acacia trees in response to stress conditions, such as drought or wounds. GA has a variety of applications within the industrial world, including the food, cosmetic, and pharmaceutical industries, acting specifically as an emulsion stabilizer, emulsifier, and thickener in pharmaceutical settings.

Important amino acids

Amino Acids provide important interactions for binding. The side chain, providing stabilizing assistance. ^[3]. Amino Acid Residues form a hydrogen bond with the O-1 atom of Rha, suggesting these residues play a catalytic role for the elimination reaction.

Structural highlights

Secondary Structure: In this protein, there are around 30 anti-parallel beta sheets, two small hydrophobic alpha helices, and one alpha helix. The anti-parallel beta sheets provide further stabilization, through strong hydrogen bonding in the backbone, of the protein compared to parallel beta sheets. The hydrophobic alpha helices provide structure for the formation of the active site. Provided is the protein structure in space fill. This structure representation depicts the depths of the active site, showing how tightly bound the ligand is to the protein. This representation also shows what size molecule fit into the active site, giving scientists an idea of other similar-sized ligands that may also fit into this binding pocket.

Other important features

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.