Bioinformatic study on the structure of catechol 1,2 deoxygenase in Paenarthrobacter nitroguajacolicus strain Znu14

The catechol 1,2 deoxygenase is an important enzyme in the bioremediation which is capable of cataliysing the aromatic compounds. In this study, the structure of ctechol 1,2 deoxygenase in Paenarthrobacter nitroguajacolicus strain Znu14 was investigated and corresponded with the similar protein sequences, which 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. Overall, based on the comparison of parameters including index instability and hydrophobic protein interactions, it seems that the stability of the constructed protein model was structurally and functionally lower than that of template protein.

Keywords:

Aromatic compounds , Bioremediation , Catechol 1 , 2 dioxygenases , Modelling , Paenarthrobacter nitroguajacolicus