Homology modeling, simulation and molecular docking studies of catechol-2, 3-Dioxygenase from Burkholderia cepacia: Involved in degradation of Petroleum hydrocarbons

Catechol 2, 3-dioxygenase is present in several types of bacteria and undergoes degradation of environmental pollutants throughan important key biochemical pathways. Specifically, this enzyme cleaves aromatic rings of several environmental pollutants suchas toluene, xylene, naphthalene and biphenyl derivatives. Hence, the importance of Catechol 2, 3-dioxygenase and its role in thedegradation of environmental pollutants made us to predict the three-dimensional structure of Catechol 2, 3-dioxygenase fromBurkholderia cepacia. The 10ns molecular dynamics simulation was carried out to check the stability of the modeled Catechol 2, 3-dioxygenase. The results show that the model was energetically stable, and it attains their equilibrium within 2000 ps of productionMD run. The docking of various petroleum hydrocarbons into the Catechol 2,3-dioxygenase reveals that the benzene, O-xylene,Toluene, Fluorene, Naphthalene, Carbazol, Pyrene, Dibenzothiophene, Anthracene, Phenanthrene, Biphenyl makes stronghydrogen bond and Van der waals interaction with the active site residues of H150, L152, W198, H206, H220, H252, I254, T255,Y261, E271, L276 and F309. Free energy of binding and estimated inhibition constant of these compounds demonstrates that theyare energetically stable in their binding cavity. Chrysene shows positive energy of binding in the active site atom of Fe. ExceptPyrene all the substrates made close contact with Fe atom by the distance ranges from 1.67 to 2.43 Å. In addition to that, the abovementioned substrate except pyrene all other made π-π stacking interaction with H252 by the distance ranges from 3.40 to 3.90 Å.All these docking results reveal that, except Chrysene all other substrate has good free energy of binding to hold enough in theactive site and makes strong VdW interaction with Catechol-2,3-dioxygenase. These results suggest that, the enzyme is capable ofcatalyzing the above-mentioned substrate.