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Online Journal of Bioinformatics ©
Volume 17(1):13-28, 2016
In silico 3D structure of pectin lyase proteins of Aspergillus flavus NRRL 3357
AK Dubey1, S Yadav1, A Tanveer1, G Anand1, V K Singh2 and D Yadav1
1Department of Biotechnology D.D.U Gorakhpur University, Gorakhpur, 2Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, India.
Dubey AK, Yadav S, Tanveer A, Anand G Singh VK, Yadav D. Pectin., In silico 3D structure of pectin lyase protein of Aspergillus flavus NRRL 3357, Onl J Bioinform., 17(1):13-28, 2016. Lyase enzymes degrade pectin polymers forming 4,5-unsaturated oligogalacturonides. Seven pectin lyase genes retrieved from sequenced genome of A. flavus NRRL3357 were subjected to homology search, multiple sequence alignment, motif search, phylogenetic tree construction and 3D structure prediction. There were highly conserved amino acid residues at several positions and two major clusters in a phylogenetic tree. 3D structure was predicted by homology modelling using 1QCXA as a template validated by computation tools for consistency and reliability. PMDB identifier numbers for 3D models of Afpnl-2, Afpnl-3, Afpnl-4, Afpnl-5, Afpnl-6 and Afpnl-7 were PM0078057, PM0078058, PM0078048, PM0078049, PM0078059 and PM0078060 respectively. Secondary structure of these pectin lyases revealed variability in terms of number of strands, helices, β-turns, γ turns and disulphide bonds. pH ranged acidic for Afpnl-5 to alkaline for Afpnl-2 proteins and aliphatic index from 67.73 for Afpnl4 to 79.39 for Afpnl2. The ubiquitous presence of Pec_Lyase_C domain among these proteins along with highly conserved amino acid residues as revealed by multiple sequence alignment confirmed identity.
Key Words: Pectin lyase, Aspergillus flavus,In silico, Three dimensional structure, Homology modeling, template.