Cutinases (E.C. 3.1.1.74) are hydrolytic enzymes, member of α/β hydrolase superfamily, that degrade insoluble biopolyester cutin, which is the structural component of plant cuticles. Because of the multifunctionality of cutinase enzymes, they are used in several fields such as in food, agriculture, detoxification, dairy product, textile, laundry, chemicals, and pharmaceutical industry. Cutinases are produced by phytopathogenic fungi and bacteria. In contrast to fungal cutinases, relatively little is known about these enzymes from bacterial sources. The role of cutinase has been shown to facilitate the mode of entry of PGPR (Plant Growth-Promoting Rhizobacteria) endophytes into the newly emerged lateral roots or utilized root hairs. PGPR have emerged during the last decades as a potent alternative to chemical fertilizers, pesticides, and other supplements in an eco-friendly agriculture. Among these bacteria that have an agricultural interest, Pseudomonas fluorescens is the subject of particular attention. The aim of the study was to better understand and identify the three-dimensional (3-D) structure and properties of cutinase protein from P. fluorescens by using bioinformatics tools. Basic physicochemical characteristics were analyzed using Expasy’s Protparam and ProtScale tools. Several physicochemical characteristics of the cutinase enzyme were demonstrated. The instability index value indicated that the protein was highly stable. Furthermore, no transmembrane domain and no peptide signal were found in the protein, and the enzyme has a cytoplasmic localization. Secondary structure analysis was carried out by both SOPMA and PSIPRED programs that revealed that random coil dominated among secondary structure elements followed by α-helix, extended strand, and β-turn. Moreover, tertiary structure prediction was analyzed by Phyre2 server based on homology modeling and the predicted model was refined by ModRefiner and validated using PROCHECK’S Ramachandran plot. Ramachandran plot analysis showed that 89.2% of amino acid residues are within the most favored regions. Prediction of enzyme binding site by COFACTOR server was confident with a BS-score > 0.5. Protein-protein interaction networks demonstrated that cutinase of interacted with seven other proteins in a high confidence score. Overall, this in silico analysis study provides insights about physicochemical properties, structure, and function of cutinase from P. fluorescens, which would help to produce the enzyme on a large scale allowing its wide exploiting in various industrial and agricultural products and processes.

Cutinase, Pseudomonas fluorescens, in silico analysis, homology modeling

biology

Presentation: None