In silico characterization of bacterial chitinase: illuminating its relationship with archaeal and eukaryotic cousins

Abstract

Background Chitin is one of the most abundant biopolymers on Earth, only trailing second after cellulose. The enzyme chitinase is responsible for the degradation of chitin. Chitinases are found to be produced by wide range of organisms ranging from archaea to higher plants. Though chitin is a major component of fungal cell walls and invertebrate exoskeletons, bacterial chitinase can be industrially generated at low cost, in facile downstream processes at high production rate. Microbial chitinases are more stable, active, and economically practicable compared to the plant- and animal-derived enzymes. Results In the present study, computationally obtained results showed functional characteristics of chitinase with particular emphasis on bacterial chitinase which is fulfilling all the required qualities needed for commercial production. Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. Considering one suitable exemplary sequence from each group is being compared with others. Primary, secondary, and tertiary structures are determined by in silico models. Different physical parameters, viz., pI, molecular weight, instability index, aliphatic index, GRAVY, and presence of functional motifs, are determined, and a phylogenetic tree has been constructed to elucidate relationships with other groups of organisms. Conclusions This study provides novel insights into distribution of chitinase among four groups and their characterization. The results represent valuable information toward bacterial chitinase in terms of the catalytic properties and structural features, can be exploited to produce a range of chitin-derived products.

In silico comparative structural and functional analysis of arsenite methyltransferase from bacteria, fungi, fishes, birds, and mammals

“…Excessive random coils indicate that protein showed many conserved regions with evolutionary significance. Random coils sometimes give more flexibility to protein [ 31 ].

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Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention

“…The negative score of GRAVY indicated that the ADC protein could be globular in nature. Also, negative GRAVY value supports that ADC is hydrophilic in nature [ 41 ]. The instability index was found greater than 40 which suggested the thermostability of protein [ 41 ].…”

“…Also, negative GRAVY value supports that ADC is hydrophilic in nature [ 41 ]. The instability index was found greater than 40 which suggested the thermostability of protein [ 41 ]. The evolutionary relationship of arginine decarboxylase in Salinicoccus with different clusters revealed its genetic similarity and diversity over time.…”

Streptomyces sp. Strain PBR11, a Forest-Derived Soil Actinomycetia with Antimicrobial Potential

“…The predicted pathway product of the biosynthetic gene of strain PBR11 was identified using SBSPKSv2 ( 112 ). The secondary structures of the polyketide ketosynthase domains and the chitinase gene were created using the PDBsum tool ( 113 ).…”