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Domain analysis of 3 Keto Acyl-CoA synthase for structural variations in Vitis vinifera and Oryza brachyantha using comparative modelling

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Abstract

The long chain fatty acids incorporated into plant lipids are derived from the iterative addition of C2 units which is provided by malonyl-CoA to an acyl-CoA after interactions with 3-ketoacyl-CoA synthase (KCS), found in several plants. This study provides functional characterization of three 3 ketoacyl CoA synthase like proteins in Vitis vinifera (one) and Oryza brachyantha (two proteins). Sequence analysis reveals that protein of Oryza brachyantha shows 96% similarity to a hypothetical protein in Sorghum bicolor; total 11 homologs were predicted in Sorghum bicolor. Conserved domain prediction confirm the presence of FAE1/Type III polyketide synthase-like protein, Thiolase-like, subgroup; Thiolase-like and 3-Oxoacyl-ACP synthase III, C-terminal and chalcone synthase like domain but very long chain 3-keto acyl CoA domain is absent. All three proteins were found to have Chalcone and stilbene synthases C terminal domain which is similar to domain of thiolase and β keto acyl synthase. Its N terminal domain is absent in J3M9Z7 protein of Oryza brachyantha and F6HH63 protein of Vitis vinifera. Differences in N-terminal domain is responsible for distinguish activity. The J3MF16 protein of Oryza brachyantha contains N terminal domain and C terminal domain and characterized using annotation of these domains. Domains Gcs (streptomyces coelicolor) and Chalcone-stilbene synthases (KAS) in 2-pyrone synthase (Gerbera hybrid) and chalcone synthase 2 (Medicago sativa) were found to be present in three proteins. This similarity points toward anthocyanin biosynthetic process. Similarity to chalcone synthase 2 reveals its possible role in Naringenine and Chalcone synthase like activity. In 3 keto acyl CoA synthase of Oryza brachyantha. Active site residues C-240, H-407, N-447 are present in J3MF16 protein that are common in these three protein at different positions. Structural variations among dimer interface, product binding site, malonyl-CoA binding sites, were predicted in localized combination of conserved residues.

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Abbreviations

ACP:

Acyl carrier protein

CHS:

Chalcone synthase

FA:

Fatty acid

KCS:

3 keto acyl CoA Synthase

Gcs:

Germicidin synthase

PS:

Pyrone synthase

PKS:

polyketide synthase

J3M9Z7 ORYBR & J3MFI6 ORYBR:

3 keto acyl CoA Synthase like protein in Oryza brachyantha

F6HH63 VITVI:

3 keto acyl CoA Synthase in Vitis vinifera

VLCFA:

Very long chain fatty acids

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Authors and Affiliations

  1. Department of Bioinformatics, University Institute of Engineering and Technology, Chhatrapati Shahuji Maharaj University, Kanpur, 208024, India

    Mamta Sagar, Neetesh Pandey, Naseha Qamar, Brijendra Singh & Akanksha Shukla

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  1. Mamta Sagar
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  2. Neetesh Pandey
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  3. Naseha Qamar
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  4. Brijendra Singh
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  5. Akanksha Shukla
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Correspondence to Mamta Sagar.

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Sagar, M., Pandey, N., Qamar, N. et al. Domain analysis of 3 Keto Acyl-CoA synthase for structural variations in Vitis vinifera and Oryza brachyantha using comparative modelling. Interdiscip Sci Comput Life Sci 7, 7–20 (2015). https://doi.org/10.1007/s12539-013-0017-8

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