scholarly journals Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerantPseudomonassp. AMS8

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4347 ◽  
Author(s):  
Lawal Garba ◽  
Mohamad Ariff Mohamad Yussoff ◽  
Khairul Bariyyah Abd Halim ◽  
Siti Nor Hasmah Ishak ◽  
Mohd Shukuri Mohamad Ali ◽  
...  

Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacterial membrane fatty acid desaturases are not available, relevant information about the enzymes are derived from their amino acid sequences, site-directed mutagenesis and domain swapping in similar membrane-bound desaturases. The cold-tolerantPseudomonassp. AMS8 was found to produce high amount of monounsaturated fatty acids at low temperature. Subsequently, an active Δ9-fatty acid desaturase was isolated and functionally expressed inEscherichia coli. In this paper we report homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerantPseudomonassp. AMS8 for the first time to the best of our knowledge. Three dimensional structure of the enzyme was built using MODELLER version 9.18 using a suitable template. The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. The structure was subjected to energy minimization and checked for correctness using Ramachandran plots and ERRAT, which showed a good quality model of 91.6 and 65.0%, respectively. The protein model was used to preform MD simulation and docking of palmitic acid using CHARMM36 force field in GROMACS Version 5 and Autodock tool Version 4.2, respectively. The docking simulation with the lowest binding energy, −6.8 kcal/mol had a number of residues in close contact with the docked palmitic acid namely, Ile26, Tyr95, Val179, Gly180, Pro64, Glu203, His34, His206, His71, Arg182, Thr85, Lys98 and His177. Interestingly, among the binding residues are His34, His71 and His206 from the first, second, and third conserved histidine motif, respectively, which constitute the active site of the enzyme. The results obtained are in compliance with thein vivoactivity of the Δ9-fatty acid desaturase on the membrane phospholipids.

2021 ◽  
Vol 22 (19) ◽  
pp. 10857
Author(s):  
Nadia Raboanatahiry ◽  
Yongtai Yin ◽  
Kang Chen ◽  
Jianjie He ◽  
Longjiang Yu ◽  
...  

Fatty acid desaturases add a second bond into a single bond of carbon atoms in fatty acid chains, resulting in an unsaturated bond between the two carbons. They are classified into soluble and membrane-bound desaturases, according to their structure, subcellular location, and function. The orthologous genes in Camelina sativa were identified and analyzed, and a total of 62 desaturase genes were identified. It was revealed that they had the common fatty acid desaturase domain, which has evolved separately, and the proteins of the same family also originated from the same ancestry. A mix of conserved, gained, or lost intron structure was obvious. Besides, conserved histidine motifs were found in each family, and transmembrane domains were exclusively revealed in the membrane-bound desaturases. The expression profile analysis of C. sativa desaturases revealed an increase in young leaves, seeds, and flowers. C. sativa ω3-fatty acid desaturases CsaFAD7 and CsaDAF8 were cloned and the subcellular localization analysis showed their location in the chloroplast. They were transferred into Arabidopsis thaliana to obtain transgenic lines. It was revealed that the ω3-fatty acid desaturase could increase the C18:3 level at the expense of C18:2, but decreases in oil content and seed weight, and wrinkled phenotypes were observed in transgenic CsaFAD7 lines, while no significant change was observed in transgenic CsaFAD8 lines in comparison to the wild-type. These findings gave insights into the characteristics of desaturase genes, which could provide an excellent basis for further investigation for C. sativa improvement, and overexpression of ω3-fatty acid desaturases in seeds could be useful in genetic engineering strategies, which are aimed at modifying the fatty acid composition of seed oil.


Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1983-1990 ◽  
Author(s):  
Takahiro Oura ◽  
Susumu Kajiwara

Fungi, like plants, are capable of producing the 18-carbon polyunsaturated fatty acids linoleic acid and α-linolenic acid. These fatty acids are synthesized by catalytic reactions of Δ12 and ω3 fatty acid desaturases. This paper describes the first cloning and functional characterization of a yeast ω3 fatty acid desaturase gene. The deduced protein encoded by the Saccharomyces kluyveri FAD3 gene (Sk-FAD3) consists of 419 amino acids, and shows 30–60 % identity with Δ12 fatty acid desaturases of several eukaryotic organisms and 29–31 % identity with ω3 fatty acid desaturases of animals and plants. During Sk-FAD3 expression in Saccharomyces cerevisiae, α-linolenic acid accumulated only when linoleic acid was added to the culture medium. The disruption of Sk-FAD3 led to the disappearance of α-linolenic acid in S. kluyveri. These findings suggest that Sk-FAD3 is the only ω3 fatty acid desaturase gene in this yeast. Furthermore, transcriptional expression of Sk-FAD3 appears to be regulated by low-temperature stress in a manner different from the other fatty acid desaturase genes in S. kluyveri.


2000 ◽  
Vol 28 (6) ◽  
pp. 636-638 ◽  
Author(s):  
O. Sayanova ◽  
F. Beaudoin ◽  
B. Libisch ◽  
P. Shewry ◽  
J. Napier

The consensus sequence of the third histidine box of a range of Δ5, Δ6, Δ8 and sphingolipid desaturases differs from that of the membrane-bound non-fusion Δ12 and Δ15 desaturases in the presence of glutamine instead of histidine. We have used site-directed mutagenesis to determine the importance of glutamine and other residues of the third histidine box and created a chimaeric enzyme to determine the ability of the Cyt b5 fusion domain from the plant sphingolipid desaturase to substitute for the endogenous domain of the Δ6 desaturase.


2004 ◽  
Vol 37 (2) ◽  
pp. 156-173 ◽  
Author(s):  
Andrew W. McCartney ◽  
John M. Dyer ◽  
Preetinder K. Dhanoa ◽  
Peter K. Kim ◽  
David W. Andrews ◽  
...  

2015 ◽  
Vol 57 (1) ◽  
pp. 89-99 ◽  
Author(s):  
Kenshi Watanabe ◽  
Makoto Ohno ◽  
Masahiro Taguchi ◽  
Seiji Kawamoto ◽  
Kazuhisa Ono ◽  
...  

2013 ◽  
Vol 32 (04) ◽  
pp. 445-458 ◽  
Author(s):  
Tatiana Klempova ◽  
Daniel Mihalik ◽  
Milan Certik

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