Alginate lyase lives in a salty environment with an optimal pH of 8 and temperature of 22C. This protein consists of 2 large beta-sheets and 4 alpha-helices. Beta-sheet A contains most of the catalytic amino acids. There is a mutant of the is protein with the PDB ID 7C8F. The mutant contains dimannuronate.
Function of your protein
, 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.
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 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.
The shows the four important amino acid and the hydrogen bonding.
Structural highlights
Secondary structures are . 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.
The is hydrogen bonds and a disulfide bridge. The hydrogen bonds help hold the helices together and are important in protein folding. The disulfide bridge is used to help stabilize the protein. The quaternary structure in AlyC3 is the dimer structure. A dimer is consisted of two monomers and helps increase the stability and availability of the active site.
The view shows the cleft in the protein. This cleft is where the active site is located and allows the substrate to attach.
Other important features
Alginate Lyase has a 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 from Cys169-Cys183. This is used to stabilize the tertiary and quaternary structure of the protein.
