An in silico approach for the comparative characterization of imidazolonepropionase from Agrobacterium fabrum and Bacillus subtilis: an imperative enzyme for histidine degradation

Introduction: The third step in histidine degradation is catalysed by imidazolonepropionase. It catalyses the conversion of 4-imidazolone-5-propionic acid to produce N-formimino-l-glutamic acid by hydrolyzing carbon—nitrogen bonds. The histidine is a very expensive amino acid inside the cell and its degradation is a very conserved process. To date, very few reports exist regarding the structure of bacterial imidazolonepropionase, but no reports have been published regarding the comparative structure and sequence analysis of this enzyme from bacterial sources.

Methods: An in silico study has been conducted to characterize imidazolonepropionase from gram-positive Bacillus subtilis and gram-negative Agrobacterium fabrum.

Results: The sequence analysis revealed that more charged residues are present in Bacillus subtilis. These charged residues help in the increment of the polarity and hydrophilicity of Bacillus subtilis. The formation of intra-protein interactions was also high in gram-positive species. Interestingly, both species have an almost equal abundance of aromatic amino acids in their sequences, but the formation of aromatic—aromatic interactions was high in Bacillus subtilis. Finally, the molecular dynamics simulation study revealed that imidazolonepropionase from Bacillus subtilis was more stable and compact than Agrobacterium fabrum.

Conclusion: The imidazolonepropionase from Bacillus subtilis was more stable than Agrobacterium fabrum. Due to the presence of higher stable imidazolonepropionase in Bacillus subtilis, it can use histidine more efficiently.