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Online Journal of Bioinformatics ©
Volume 11 (2): 302-316, 2010
Model ligand-binding site of 2-Amino-5-chlorophenol 1,6-dioxygenase in Comamonas sp. CNB-1.
K Monika1, D Muralidhara Rao1, N Anuraj2, M Yadav2, N Nageswara Rao and K Venkateswarlu1*
1Department of Microbiology/Biotechnology, Sri Krishnadevaraya University, Anantapur , 2Bioinformatics Research Laboratory, Eminent Biosciences, Indore, 3Department of Chemistry, MVR College of Engineering and Technology, Paritala, India
Monika K, Muralidhara Rao D, Anuraj N, Yadav M, Nageswara Rao N, Venkateswarlu K., Model ligand-binding site of 2-Amino-5-chlorophenol 1,6-dioxygenase in Comamonas sp. CNB-1, Online J Bioinformatics, 11 (2): 302-316, 2010. Comamonas sp. CNB-1 utilizes chloronitrobenzene as the sole source of carbon and nitrogen. In the reductive catabolic pathway, 2-amino-5-chlorophenol is an intermediate which is subsequently used as the substrate by meta-ring fission enzyme, 2-amino-5-chlorophenol 1,6-dioxygenase. As no crystal structure of the enzyme has yet been published, the sequences of both α-subunit (CnbCa) and β-subunit (CnbCb) of the dioxygenase from strain CNB-1 were used to generate homology models employing the templates from acetyl transferase of B. subtilis (PDB entry 1MK4) and putative dehydrogenase of E. coli (PDB entry 1QTA). The models were assessed for reliable structure by PROCHECK, ERRAT, and VERIFY-3D. In the absence of homology for the developed model of α-subunit, only a β-subunit model of the dioxygenase was docked with the physiological substrate, 2-amino-5-chlorophenol, using ProFunc tool. The results of docking studies revealed the presence of specific amino acid residues, Pro54, Lys170, Val143 and Val169, within the binding pocket, and suggested that protocatechualdehyde is the competitive inhibitor for β-subunit of the enzyme. Two inhibitor molecules, CID_21643223 and CID_11275762, appear to be suitable for interaction at the active site of β-subunit.
Keywords: 2-Amino-5-chlorophenol 1,6-dioxygenase, Comamonas sp. CNB-1, Homology modelling, Molecular docking, 2-Amino-5-chlorophenol, rotocatechualdehyde