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In Silico Structural and Functional Analyses of Bacillus Uricases

Author(s):

Anand Kumar Nelapati, Shubham Meena, Aditya Kumar Singh, Narsimha Bhakta and JagadeeshBabu PonnanEttiyappan*   Pages 1 - 19 ( 19 )

Abstract:


Background: Excluding humans, the peroxisomal uricase is responsible for the catabolism of uric acid into allantoin in many species like microorganisms, plants, and invertebrates. Particularly in humans, the synthesis and excretion of uric acid are naturally balanced. When the uric acid concentration crosses 7 mg/dl will results in conditions such as hyperuricemia and gout. Uricase is one of the potential source for the reduction of uric acid in humans. Uricase is also widely used as a commercial diagnostic reagent in medical and clinical biochemistry to estimate the uric acid concentration in blood and other biological fluids. Computational approaches can be used for the screening and investigation of a uricase enzyme with desirable characteristics that can be employed in diverse industrial applications.

Objectives: The present study deals with computational-based structural, functional, and phylogenetic analyses of uricase enzymes from various Bacillus species.

Method: Seventy uricase protein sequences from Bacillus species were selected for multiple sequence alignment, phylogenetic analysis, motif assessment, domain architecture examination, understanding of basic physicochemical properties and in silico identification of the composition of amino acids in uricase. Further, structural (secondary and tertiary structure prediction), and functional (CYS_REC, MOTIF scan, CD-search, STRING, SOSUI, and PeptideCutter) analysis of uricase were performed.

Results: Bacillus simplex (WP_063232385.1) was chosen as the representative species of the Bacillus genera. The three-dimensional (3D) structure of B. simplex uricase is predicted and validated using QMEAN, RAMPAGE, ERRAT, Verify 3D and PROQ servers. Analysis revealed that the tertiary structure of the selected uricase has good quality and acceptability.

Conclusion: Computational analysis of uricase from various Bacillus sources revealed that all the selected Bacillus uricases are active within acidic to a neutral environment, thermally stable with molecular weight ranging from 35.59-59.85kDa. The secondary structure analysis showed that all uricases are rich in alpha helices and sheets. The CDD tool identified two conserved domains, one of which belongs to OHCU decarboxylase and another to Uricase superfamily. The quality estimation of 3D modelled protein gave a high overall quality factor score of 94.64. Also, all Bacillus species of uricase enzyme and their corresponding genes showed a strong correlation from the phylogenetic comparison of the selected taxa. The present detailed computational investigation on the uricase protein could help in screening a suitable uricase producing microbe with desirable characteristics for industrial application.

Keywords:

Uricase, Bacillus species, phylogenetic analysis, secondary structure, protein modeling, in silico analysis.

Affiliation:

Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore



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