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Function of your protein

AlyC3 is an present in Psychromonas sp. C-3 that plays a role in β-elimination at the glycosidic 1,4-O-linkage in alginate. AlyC3 uses tetramannuronate or polymannuronate as its substrate and converts the polymer into its substituent monomers, shorter PM chains, and 4-deoxy-L-erythro-hex-4-enopyranosyluronic acid. This facilitates alginate degradation and recycling in marine ecosystems.

Biological relevance and broader implications

Alginate lyases are made by bacteria, viruses, fungi, marine algae, and marine molusks. The protein PL7 alginate lyase AlyC3 plays roles in the degradation and recycling of alginate in ocean ecosystems. Alginate lyases have a variety of potential applications in the food, agriculture, and pharmaceutical industries. They may even be used to treat chronic lung infections by Pseudomonas aeruginosa. Exolytic and endolytic alginate lyases working in conjunction also have the potential to produce biofuels by breaking down alginate-rich algal cell walls into its substituent monosaccharides.

Important amino acids

The residues His127, and Tyr244 are important for the catalytic function of AlyC3 as mutating either or both amino acids to an alanine resulted in an almost inactive enzyme. Arg82 and Tyr190 at the two ends of the catalytic canyon are the most important for binding and positioning the alginate substrate in AlyC3’s active site. The shown is dimannuronate complexed with a malonate ion. This fits in the on a in a β-sheet on the enzyme where H127 deprotonates the substrate and Y244 is deprotonated by the oxygen in the 1,4-O-linkage between monomers degrading the substrate.

Structural highlights

AlyC3's quaternary structure consists of two two with Cyclic – C2 symmetry. The cavity formed by a β-sheet is the most important aspect of its tertiary structure as this is where the enzyme's substrate binds. Its is approximately 14% helices (magenta) and 44% beta strands (yellow). Both domains each consist of 7 helices and 15 strands with one disulfide bridge. The most important for binding (R82,Y190) substrate as well as those involved in catalysis (H127,Y244) all lie in on beta strands in both domains of the protein. Positive charges in the groove as well as physical shape position the substrate in its active site with the WT having a Km value of 0.24 ± 0.05 (mg/ml). A view highlights the way the substrate fits in its active site on the surface of the enzyme.

Other important features

Two other (Q125,R78) are highly conserved and help mediate the catalytic reaction by interacting with the carboxyl group of the M+1 and activate the Cα hydrogen of M+1.

Another important is His141. Its hydrophilic nature is believed to be important in stabilizing the substrate in the active site as mutating this amino acid to an alanine increases the Km value to 5.28 ± 1.11 and decreases the Vmax to 6976.64 ± 852.13.

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