Bioinformatic Characterization of a Kappa-Carrageenase from Pseudomonas fluorescens

Abstract

Abstract Kappa-carrageenase (EC 3.2.1.83) is a glycoside hydrolase family 16 (GH16) member that could specifically hydrolyse kappa-carrageenans to kappa-carrageenan oligosaccharides. Kappa-carrageenase enzymes have attracted much interest due to their numerous potential applications in biomedical and physiological fields, bioethanol production, and textile industry. In the present study, physicochemical, secondary structure, structural properties including homology modeling, refinement, and model quality validation, and functional analyses of the kappacarrageenanse from Pseudomonas fluorescens using various bioinformatic tools were conducted. The protein was found to be stable and acidic in nature. Secondary structure prediction revealed that the presence of random coil is more dominated in the protein sequence followed by extended strand, α-helix, and β-turn. Protein-protein interaction prediction revealed ten potential functional partners. This bioinformatic characterization provides for the first time insights into fundamental characteristics of the predicted Kappa-carrageenase of P. fluorescens, which may be useful for elucidating its applications and for further expression and characterization studies.