title: Domain analysis of 3 Keto Acyl-CoA synthase for structural variations in Vitis vinifera and Oryza brachyantha using comparative modelling.
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.
authors.affiliation: Department of Bioinformatics, University Institute of Engineering and Technology, Chhatrapati Shahuji Maharaj University, Kanpur, 208024, India, mamta1060@yahoo.com.
authors.forename: Mamta
authors.initials: M
authors.lastname: Sagar
authors.forename: Neetesh
authors.initials: N
authors.lastname: Pandey
authors.forename: Naseha
authors.initials: N
authors.lastname: Qamar
authors.forename: Brijendra
authors.initials: B
authors.lastname: Singh
authors.forename: Akanksha
authors.initials: A
authors.lastname: Shukla
mesh_terms: D015099:3-Oxoacyl-(Acyl-Carrier-Protein) Synthase / Q000737:chemistry; D000214:Acyl Coenzyme A / Q000737:chemistry*; D000217:Acyltransferases / Q000737:chemistry; D000595:Amino Acid Sequence; D000872:Anthocyanins / Q000096:biosynthesis*; D001665:Binding Sites; D020134:Catalytic Domain; D017124:Conserved Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012275:Oryza / Q000737:chemistry* / Q000201:enzymology; D010940:Plant Proteins / Q000737:chemistry; D010944:Plants / Q000737:chemistry / Q000201:enzymology; D017434:Protein Structure, Tertiary; D011753:Pyrones / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D027843:Vitis / Q000737:chemistry* / Q000201:enzymology
chemical_list: C584017:2-pyrone; D000214:Acyl Coenzyme A; D000872:Anthocyanins; D010940:Plant Proteins; D011753:Pyrones; D000217:Acyltransferases; C022674:stilbene synthase; D015099:3-Oxoacyl-(Acyl-Carrier-Protein) Synthase; C020141:flavanone synthetase