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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 as a substrate and....

Biological relevance and broader implications

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.

Important amino acids

Alginate lyase contains a main ligand that is an oligosaccharide: The beta pleated sheets, 7 and 10, containing Gln124 (125 on Protopedia) and Tyr189 (190 on Protopedia), 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 alpha helices are shown in yellow, and the beta sheets are shown in pink. The for interaction with the substrate, mannuronate.

A space-fill view of the protein is shown , and the long 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

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.