Evaluation of the structure of catechole 2,3 deoxygenase in Aneurinibacillus migulanus strain Znu12 via bioinformatic studies

Catechol 2,3-dioxygenases is one of the enzymes degrading the aromatic compounds. There is Fe2+ in each subunit of the enzyme. The enzyme is capable of degrading phenol, benzoatet, Cholorocathechol, methilcathechol from wastewater, therefore, it has taken an attention by the industry. In the present study, the structure of Catechol 2,3-dioxygenases in Aneurinibacillus migulanus strain Znu12 was assessed by different bioinformatics instruments. For this, the similar protein sequences were obtained from NCBI server. Then, the most similar sequence to the bacterial protein was selected and its models were designed by Modeller 9v18 software. Afterwards, for further evaluations, the best model was selected based on structural parameters using ModEval, SAVES, SpdbViewer and Pic Server softwares. Moreover, for testing the accuracy of the designed model, the different interactions between the template sequence with the selected model were assessed and compared. In addition, the 3D structure of the protein was constructed using Chimera software, and the Fe-bounded active site of the enzyme was also determined.Thereby, the similarity and differences between the 3D structures of the template and model proteins were evaluated. The conserved and Fe-bounded amino acids were identified by ESPript3 server, showing the similarity between obtained protein sequence from NCBI with template and modelled protein. Finally, the model of the studied bacterial protein was constructed after corresponding of the sequence of template with the designed model sequence. It seems that, based on the comparison of parameters including index instability and hydrophobic protein interactions, the stability of the constructed protein model was structurally higher, while functionally lower, than that of template protein

Keywords:

Aromatic compounds , Aneurinibacillus migulanus , Bioremediation , Catechol 2 , 3-dioxygenases , Modelling