Comprehensive Genomic and Metabolic Profiling of ι-Carrageenase A2 from Seonamhaeicola marinus: In Silico Modeling and Molecular Dynamics for Biotechnological Applications

Seonamhaeicola marinus, a marine bacterium from the family Flavobacteriaceae, was genomically analyzed. Approximately 23% of its predicted CDSs were linked to subsystems, with amino acid and protein metabolism being the most abundant. Four biosynthetic gene clusters (BGCs) were identified, including those for flexirubin and carotenoid. CAZyme analysis via dbCAN3 revealed 178 CAZymes, representing 3.87% of the genome, with glycosyl hydrolases, particularly GH2, being the most prevalent group. Polysaccharide-producing organisms, such as those yielding carrageenan from red algae, find applications in food, cosmetics, and pharmacology. ι-Carrageenan, characterized by its double sulfate groups, holds significant potential in pharmaceutical systems. ι-Carrageenase A2 from S. marinus has desirable properties for carrageenan processing, supporting the investigation of such novel enzymes for biotechnological uses. This study aimed to comprehensively analyze S. marinus ι-carrageenase A2 through various computational modeling methods. A comparative analysis of the enzyme’s physicochemical properties, binding site locations, and structural features was conducted with other enzymes from the same family. Multiple computer modeling software programs were employed for three-dimensional structure prediction and modeling. Molecular docking identified potential ligands, with neo-ι-carratetraose demonstrating strong binding affinity. Molecular dynamics simulations assessed the stability and flexibility of the ligand-enzyme complex, offering insights into key residues involved in substrate interactions.