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 primarily found in algae and is the primary marine polysaccharides and carriers of the marine carbon cycle. Alginate lyase is synthesized by marine algae, mollusks, fungi, bacteria, and viruses.
Alginate lyase plays an important role in the treatment of lung infections, primarily in those with Cystic Fibrosis.
Alginate lyase is also important in environmental research dealing with biofuels and the recycling of alginate in the oceans.
Important amino acids
The 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 (hydrogen bonds and disulfide bridge) and Quaternary(dimer) structure
space filling view- cleft
Other important features
Alginate Lyase has a channel where the sugar sits in. This channel is positively charged for the negatively charged sugar chain. The protein cleaves the sugar at the 0 site. The mutant of alginate lyase does not cleave the sugar right away.
Alginate Lyase contains a disulfide bond from Cys169-Cys183. This is used to stabilize the tertiary and quaternary structure of the protein.
