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OJBTM
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
ABSTRACT
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