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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 that naturally breaks down and degrades Gum Arabic (GA) by releasing the Rha caps found on the non-reducing ends 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)
The enzyme in this study, FoRham1 is a mutant Rha-releasing enzyme that specifically uses a-L-rhamnose-a-1,4-D-glucuronic acid (Rha-GlcA) as a .[3] The mechanism provided in the literature shows FoRham1 removing the Rha cap from the GlcA, producing Rha sugar and GA as products. By doing this, scientist hope to be able get a better understanding of GA structure and characteristics to then advance its usefulness to society.
Biological relevance and broader implications
According to scientific literature, little is known about GA carbohydrate structure. This study is being used to understand more about the degradation/function of GA, as there is no known enzyme that can completely degrade GA. Although GA structure has been studied significantly with the use of chemical methods such as NMR and methylation, a detailed structure has not been produced as it is a complex branched polysaccharide.
Important amino acids
Amino acids His85, His105, Tyr150, Arg166, Ser170, Arg220, Pro223, Asn275, Arg331 are important in ligand to protein interaction. . [4]
His 85, Arg166, Tyr 150 are threeamino acids that form hydrogen bonds with the Rha sugar. His 85 and Arg166 proved to be a key amino acid in the catalytic reaction that divides the Rha-GlcA complex in the binding pocket during the reaction. . His 105 showed to form a stabilizing hydrogen bond with His 85, reinforcing the catalytic importance of His 85. The Rha Sugar cap on the GA also interacts with amino acids Arg166, Ser170, Arg220 by Hbonding, which is an important part of separating Rha-GlcA.
Amino Acids Asn275 and Arg331 Hbond with the Glc, and they play an important role in stabilization during the catalytic mechanism.
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.
