Sandbox Reserved 1693

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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

The protein, L-rhamnose-a-1,4-D-glucuronate lyase, is an enzyme from the fungus Fusarium oxysporum 12S (FoRham1) that potentially naturally breaks down and degrades Gum Arabic (GA) by releasing the Rha caps found on the non-reducing ends of GA. According to the study, little is known about GA carbohydrate structure, so this study is being used to understand more about how to degrade/function of GA. I chose to specifically look at the mutant H105F Rha-GlcA ligand which has a PDB file: 7ESN. A colored image of this can be seen (For Reference N-5' = Blue, C-3' = Red)

Biological relevance and broader implications

Important amino acids

Amino acids His85, Tyr150, Arg166, Ser170, Arg220, Pro223, Asn275, Arg331 are important in ligand to protein interaction. . His 85 and Tyr 150 are two amino acids that form hydrogen bond with the Rha sugar and His 85 proved to be a key amino acid in the catalytic reaction that separates the Rha-GlcA complex in the binding pocket. His 105 showed to form a stabilizing hydrogen bond with His 85, reinforcing the catalytic importance of His 85. ^[3]

Structural highlights

Secondary Structural Highlights - I found that there are lot of long antiparallel beta sheets in the protein (approx. 30 Beta sheets). I also observed that there was one larger alpha helix, with two smaller hydrophobic helices in the protein structure. This could mean that the protein is very stable, as antiparallel sheets provide more structure stabilization compared to parallel beta sheets. This is all due to how Hbonding between backbones occur. I also have observed that many of the beta sheets are formed of polar amino acids, which plays a role in how the protein folds.

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.