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OJBTM
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.
ABSTRACT
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.