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Function of your protein

The protein, , is from the Arctic brown alga, Laminara. Alginate lyase is an important enzyme for breaking down alginate in the ocean; alginate is a protein with unique gel-forming properties. The alginate lyase enzyme binds tetramannuronate and polymannuronate as substrates and generates oligosaccharide or monosaccharide products.

Biological relevance and broader implications

Studying alginate lyase is crucial to the understanding of how alginate is degraded and recycled in the ocean and to the development of their use for human benefit. Alginate lyases are an important element of the pharmaceutical industry as they can be used to treat chronic pulmonary infections such as cystic fibrosis (CF). The pathogen, Pseudomonas aeruginosa, infects the airway of CF patients and causes excessive lung inflammation, mucus blockage in the airway, and quick declines in overall lung function. Alginate lyase has been shown to participate in detachment of Pseudomonas aeruginosa from bacterial biofilms in the airway.

This particular protein is important to study because little is known about the alginate lyases that originate from cold polar environments. These alginate lyases from the Arctic ocean have some unique mechanisms for adaptation and alginate degradation.

Important amino acids

The amino acids Arg78, Arg82, Gln125, His127 (Ala127 in mutant), Tyr190, and Tyr244 (Ala244 in mutant) are all the substrate. The catalytic amino acids for alginate lyase (AlyC3) are normally His127 and Tyr244, but this is the mutant alginate lyase, which has of Ala127 and Ala244. The , Arg78, Arg82, and Tyr190, is involved in accurate positioning of the substrate polymer in the catalytic center.

Another view of the protein's active site can be seen . The catalytic amino acids (Ala127, Ala244) are shown in blue, catalytic triad (Arg78, Arg82, Tyr190) is shown in purple, and Gln125 (important for hydrogen bonding) is shown in orange.

Alginate lyase contains a main ligand/substrate that is a The beta pleated sheets, 7 and 10, containing Gln125 and Tyr190, respectively, form with the main ligand.

Structural highlights

Alginate lyase is a (contains two domains). One domain is shown in blue, and the other is in green. Being in a dimer form allows the protein to adapt to the seawater salinity of the Arctic ocean from which is originates. The protein's tertiary structure is held together by many hydrogen bonds and some cation-pi interactions. Each domain of the protein is made of . The for interaction with the substrate, mannuronate. One beta sheet is called sheet A, and the other is sheet B. Sheet A consists of 9 beta strands, and sheet B consists of 7 beta strands; you can see the distinction between the two strands (sheet A = pink, sheet B = orange). and forms a positively charged groove where the substrate binds.

A space-fill view of the protein is shown , and the cleft in the blue domain can be seen where the substrate binds to the active site. The cleft is a long valley-like groove that is positively charged for the negatively charged long-chained sugar substrate to sit in. The space-fill view also clearly displays the two domains of the protein.

Other important features

As seen in the image below, the protein has two active centers since it is a dimer. In the "front view of the active center," it can be seen that each active center is made of positively charged amino acids (blue) important for binding the negatively charged substrate. As seen in the "back view of the active center," the rest of the protein not containing the active site is evenly distributed with positive and negative charges because the substrate does not bind there.

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.