BACK TO CONTENTS   |    PDF   |    PREVIOUS   |    NEXT

Title

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

 

Authors

AT Ajao1*, M Kannan2, R Krishna2, SE Yakubu3, VJ Umoh3 & JB Ameh3

 

Affiliation

1Department of Biology, Institute of Basic & Applied Sciences Kwara State Polytechnic, Ilorin, Nigeria; 2Centre for Bioinformatics, Pondicherry University, Puducherry-605014, India; 3Department of Microbiology, Ahmadu Bello University, Zaria, Nigeria.

 

Email

ajaoabdullahi@yahoo.com; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received August 05, 2012; Accepted August 14, 2012; Published September 21, 2012

 

Abstract

Catechol 2, 3-dioxygenase is present in several types of bacteria and undergoes degradation of environmental pollutants through an important key biochemical pathways. Specifically, this enzyme cleaves aromatic rings of several environmental pollutants such as toluene, xylene, naphthalene and biphenyl derivatives. Hence, the importance of Catechol 2, 3-dioxygenase and its role in the degradation of environmental pollutants made us to predict the three-dimensional structure of Catechol 2, 3-dioxygenase from Burkholderia 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 production MD 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 strong hydrogen 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 they are energetically stable in their binding cavity. Chrysene shows positive energy of binding in the active site atom of Fe. Except Pyrene all the substrates made close contact with Fe atom by the distance ranges from 1.67 to 2.43 . In addition to that, the above mentioned substrate except pyrene all other made p-p stacking interaction with H252 by the distance ranges from 3.40 to 3.90 . All these docking results reveal that, except Chrysene all other substrate has good free energy of binding to hold enough in the active site and makes strong VdW interaction with Catechol-2,3-dioxygenase. These results suggest that, the enzyme is capable of catalyzing the above-mentioned substrate.

 

Keywords

Catechol-2, 3-dioxygenase, hydrocarbons, Docking,oil spills, active residues, MD simulation

 

Citation

Ajao et al. Bioinformation 8(18): 848-854 (2012)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.