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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 enzyme is 7ESM from PDB. A crystal structure of a from the fungi Fusarium oxysporum highlights the structure of the enzyme and its ligand (RAM 601). The main function of the enzyme is to lyse the L-rhamnose from the end caps of non-reducing ends of the Gum Arabic (GA) carbohydrate complex. By lysing the L-rhamnose, the structure of GA is able to be revealed which no one has been able to see the structure of GA before. The enzyme has one ligand of relevance, the RAM connected at the active site of the enzyme labeled Ligand RAM 601.
Biological relevance and broader implications
Typically, the normal biological function of this enzyme is to be used in digestion of GA. Fusarium Oxysporum specifically uses GA as its only source of carbon. The enzyme is unrivaled by any other naturally made enzyme at lysing the L-rhamnose from Gum Arabic carbohydrate complexes. When it is purified and enough of it is created to saturate the substrate, it is capable of lysing up to 95% of all L-rhamnose from the GA complex. Its efficiency has important scientific implications, as it may provide a way for scientists to further study GA carbohydrate structures which has yet to be seen.
Important amino acids
The alpha-L-rhamnopyranose is a ligand bound to the active site of the GA-specific L-rhamnose-alpha-1,4-D-glucaronate lyase (7ESM) complex.
Here we can see the sctive site in which 8 amino acids work in conjunction with one another to bind to the alpha-L-rhamnose ligand. The Active site includes Tyr28, Gly86, His87, Tyr152, Arg222, Asn277, Gln278, and Arg333 labelled as the amino acid followed by the sequence number of the amino acid in reference to the protein.
Basically, these two images help illustrate the important features of the enzyme mainly the active site and the ligand. The Bond types are all hydrogen bound to the ligand.
Structural Highlights
includes the anti-parallel beta-pleated sheets in blue and the alpha-helices are in green.
reveals the enzymes 3D structure and displays the proteins almost cylindrical shape.
reveals that the structure of the protein is much more dense and also better illustrates where the ligand-binding site is.
shows the regions in red display hydrophobic characteristics and as you can see there is no clear pattern or order to the enzymes structure indicating it is in between hydrophobic and hydrophilic.
shows the concentration of red oxygen molecules in the center of the enzyme.
shows the different charges of certain regions of the enzyme. Red negative and blue positive.
is an image of a color coordination of amino acids in order of the protein and it flows pretty uniformly
Other important features
includes an oligosaccharide chain which acts as an L-rhamnose stabilizer and links them together in a chain and assuming the function of the sugar chain is later used as an energy source for the fungi later.
includes the sodium ion and acetate ion that act as ligand stabilizers to the protein. They basically help with the strength of ligand-binding for the protein.
Overall these structures are important in the metabolic uses of this protein and without them the enzymatic function of the protein may diminish as a result.
