Sandbox Reserved 1672

This protein has 2 large beta-sheets and 4 alpha-helices. The , binds with beta-sheet A. Beta-sheet A also contains most of the catalytic amino acids.

Function of your protein

Alginate lyase, AlyC3, comes from the Psychromonas organism. It is found mainly in algae.

The function of AlyC3 is to degrade alginate. AlyC3 plays a role in b-elimination at the glycosidic 1,4-O link. This generates oligosaccharides or monosaccharides.

• insert rotating image of AlyC3 as a cartoon*

The known substrate for AlyC3 is polymannuronate (PM) and tetramannuronate.

Biological relevance and broader implications

Alginate is a linear polysaccharide present in great abundance in brown seaweeds, accounting for ;40% dry weight of brown algae (1). Brown seaweeds are the most productive algae in marine ecosystems. For example, kelp forests produce large amounts of biomass rapidly, forming the basis of coastal food webs and constituting an important carbon sink (2). Therefore, alginate is an important marine polysaccharide and carrier of the marine carbon cycle. In addition to brown algae, alginate

Alginate lyases are

promising enzymes for the treatment of chronic lung infection by Pseudomonas aeruginosa (9). The synergistic action of endoand exolytic alginate lyases have remarkable potential for the production of biofuels by deconstructing the alginate-rich algal cell walls into monosaccharides (10, 11). Therefore, research on the characteristics and molecular catalytic mechanisms of alginate lyases is important to understand the degradation and recycling of alginate in the ocean and to facilitate the development of their industrial applications.

Important amino acids

The ligands present in AlyC3 are the same as the substrate, polymannuronate and tetramannuronate, both sugars.

The catalytic amino acids in the binding site are His127 and Tyr 244. (Figure E) These residues act as the catalytic acid and base for the reaction. Tetramannuronate is cleaved in the active site and produces trisaccharides and monosaccharides.

Arg78 and Gln125 are also present and work to neutralize the negative charge on the carboxylic group.

Figure 5D shows the active site. show the catalytic triad amino acids and hydrogen bond with beta-sheets

Structural highlights

Secondary structures are alpha-helices and beta-sheets. The alpha helices are identified with the red color and the beta-sheets are identified with the blue color. There are two beta-sheets with 9 beta-strands in one and 7 beta-strands in the other. These sheets create what is called a jelly-roll fold with antiparallel strands and a hydrophobic interface. The secondary structures provide shape for the protein by creating a cleft and positively charged groove.

Tertiary and Quaternary structure

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.