Title:<i>In Silico</i> Structural and Functional Analysis of <i>Bacillus</i> Uricases
VOLUME: 18 ISSUE: 2
Author(s):Anand Kumar Nelapati, Shubham Meena, Aditya Kumar Singh, Narsimha Bhakta and JagadeeshBabu PonnanEttiyappan*
Affiliation:Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025
Keywords:Uricase, Bacillus species, phylogenetic analysis, secondary structure, protein modeling, in silico, analysis.
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, it results in conditions such as hyperuricemia
and gout. Uricase is one of the potential sources 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 screening and investigation of 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.
Methods: 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) analyses 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 was predicted and validated
using QMEAN, RAMPAGE, ERRAT, Verify 3D and PROQ servers. The 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, and thermally stable
with a 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 belongs to Uricase superfamily.
The quality estimation of 3D modeled 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.
