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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
This is a picture of my protein, L-rhamnose-alpha-1,4-D-glucuronate lyase, with The Ligand highlighted as shown. Our protein’s main function is to degrade GA and can be found in Fusarium oxysporum, a phytopathogenic fungus that uses GA as the sole carbon source for growth. It “hydrolyzes the glycosidic linkages of α-L-
rhamnose-(1→4)-D-glucuronic acid (Rha–GlcA) present in GA side chains to release Rha through
an anomer-retaining mechanism” (Kondo).
Biological relevance and broader implications
Understanding the function and mechanism of this protein will allow us to create a solid foundation in the future for carbohydrate-related enzymes. This can eventually lead to using this enzyme's mechanism and target for medicinal advancement to help treat Batten's disease, which can cause death from the inability to excrete waste from the body via the form of lipids and proteins. The information obtained by this study associated with it will tell us more about the metabolic activity of the enzyme, which will allow us to use its properties for "elucidating its physiological function in plants" (Kondo)
Important amino acids
I have included a picture of my here. The catalytic triad of my active site include the amino acids . Additionally, it was concluded that His48 was considered the catalytic residue of the active site. which switches to Q with mutations in the organism that causes death. I have included a list of the important interactions in the active site that are not as major as the active site interactions.
H- bond to Ser170
H-bond to Arg220
H-bond to Pro223
H-bond to Arg166
H-bond to Tyr15
However, the article explains that His48 is the catalytic amino acid for the mechanism of this reaction.
Structural highlights
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The hydrophobic regions of the protein are extremely important to the mechanism of this protein as the reaction is dependent on the hydrogen bonding taking place at the active site.
Other important features
This Asn provides hydrogen bonding for the structure.
