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Online Journal of Bioinformatics ©
Volume 11 (1): 38-46, 2010.
Phylogenetic Clustering and Comparative Homology Modelling of Nitrobenzene Nitroreductase
from Pseudomonas pseudoalcaligenes JS45 and Comamonas sp. CNB-1
Monika K1, Dowlathabad MR2, Spain JC3, Kadiyala V1,2*
1Department of Microbiology 2Department of Biotechnology, Sri Krishnadevaraya University, Anantapur IndiaA and 3School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
Monika K, Dowlathabad MR, Spain JC, Kadiyala V., Phylogenetic Clustering and Comparative Homology Modelling of Nitrobenzene Nitroreductase from Pseudomonas pseudoalcaligenes JS45 and Comamonas sp. CNB-1, Onl J Bioinform, 11 (1): 38-46, 2010. The nitroreductase from nitrobenzene-degrading Pseudomonas pseudoalcaligenes JS45 and chloronitrobenzene-degrading Comamonas sp. CNB-1 was used for phylogenetic analysis and comparative homology modelling. The phylogenetic dendrogram for primary sequences of nitrobenzene nitroreductase revealed high similarities (88%) in both the bacteria. The secondary structure analysis, in terms of α-helix, β-extended sheets and random coils, also showed a greater similarity in per cent occurrence of amino acids (alanine, leucine and arginine) with varying structural arrangements in the enzyme. Furthermore, using crystal structure of the nitroreductase of Bacillus cereus as a template, 3D models of the enzyme in both the strains were generated to evaluate the structural and functional relationships. The catalytic sites of the enzyme in both the bacteria are the same, while functional sites are totally different.
Key words: Nitrobenzene nitroreductase, Homology modelling, Catalytic sites, Pseudomonas pseudoalcaligenes JS45, Comamonas sp. CNB-1