Functional and bioinformatic characterisation of sequence variants of Fad3 gene from flax

Abstract

Background: Desaturases are enzymes that drive the multi-step fatty acid biosynthetic pathway. As evident from directed mutagenesis, single base changes in their polypeptide can potentially alter their structure and may result in altered substrate specificity, regioselectivity and even loss of function. The authors have previously isolated several sequence variants of Δ15 desaturase from flax while attempting to clone that gene. The aim of the present study was to analyse these gene variants for their functionality and to predict the tertiary structure of the protein in order to correlate the functional differences with the protein structure. Results: The variants differed in the rate at which they could convert linoleic acid to α-linolenic acid. The highest conversion rate was 7.03%, while the lowest was 2.39%. The overall shape of the predicted 3D model of the protein is a compact cylinder containing α-helices and β-sheets. The Ramchandran plot of this model revealed that 98.5% of the residues are located in allowed region, which denotes a stable structure. Conclusion: Although the structures of the variants are apparently similar, subtle changes account for variation in their activity. Besides, these substitutions may alter their cross-talk with other proteins and thus differentially influence their specificity, localisation and stability, which in turn may explain the diversity in their function. © 2011 Society of Chemical Industry.