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Molecular Cloning and Structural Insights into pectin lyase proteins from different strains of Fusarium

Author(s):

Sangeeta Yadav*, Gautam Anand, Vinay K Singh and Dinesh Yadav   Pages 1 - 14 ( 14 )

Abstract:


Pectin lyaseis an industrially important enzymeof pectinase group that degrade pectin polymers forming 4,5-unsaturated oligogalacturonides. Several fugal pectin lyase genes predominately from Aspergillus and Penicillium genera have been reported in the literature. Five pectin lyase genes were cloned from FusariumoxysporumMTCC1755, F.monoliforme var. subglutinansMTCC2015, FusariumavneceumMTCC10572, and FusariumsolaniMTCC3004 using PCR approach. Pectin lyase genes and proteins were subjected to homology search, multiple sequence alignment, motif search, physio-chemical characterization, phylogenetic tree construction, 3D structure prediction and molecular docking. Many conserved amino acids were found at several positions in all the pectin lyase proteins. Phylogenetic analysis of these proteins alongwith other pectinases revealed two major clusters representing members of lyases and hydrolases. In-silico characterization revealed pectin lyase proteins to be highly stable owing to the presence of disulfide bonds in their structure. Molecular weight and pI of these proteins were in the range 14.4 to 25.1 kDa and 4.47-9.39 respectively. Pectin lyase proteins from different Fusariumstrains were very much similar in their structural features and biochemical properties which might be due to their similarity on the primary sequence. Docking studies revealed that electrostatic forces, vander Waal and hydrogen bonds are the major interacting forces between the ligands and the enzyme. This might be accountable for comparatively higher and better activity of pectin lyase against galacturonic acid as compared to α-D-galactopyranuronic acid, galactofuranuronicacid and galactopyranuronate. Aspartate, tyrosine and tryptophan residues in the active site of the enzyme are responsible for ligand binding.

Keywords:

Pectin lyases, Fusarium, Cloning, Bioinformatics, Docking, 3D structure

Affiliation:

Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur (U.P.) 273 009, Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur (U.P.) 273 009, Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi (U.P.) 221 005, Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur (U.P.) 273 009



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