Structure and functional annotation of hypothetical proteins having putative Rubisco activase function from Vitis vinifera |
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Authors: | Suresh Kumar |
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Institution: | Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia |
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Abstract: | Rubisco is a very large, complex and one of the most abundant proteins in the world and comprises up to 50% of all soluble protein
in plants. The activity of Rubisco, the enzyme that catalyzes CO2 assimilation in photosynthesis, is regulated by Rubisco activase
(Rca). In the present study, we searched for hypothetical protein of Vitis vinifera which has putative Rubisco activase function. The
Arabidopsis and tobacco Rubisco activase protein sequences were used as seed sequences to search against Vitis vinifera in
UniprotKB database. The selected hypothetical proteins of Vitis vinifera were subjected to sequence, structural and functional
annotation. Subcellular localization predictions suggested it to be cytoplasmic protein. Homology modelling was used to define the
three-dimensional (3D) structure of selected hypothetical proteins of Vitis vinifera. Template search revealed that all the
hypothetical proteins share more than 80% sequence identity with structure of green-type Rubisco activase from tobacco,
indicating proteins are evolutionary conserved. The homology modelling was generated using SWISS-MODEL. Several quality
assessment and validation parameters computed indicated that homology models are reliable. Further, functional annotation
through PFAM, CATH, SUPERFAMILY, CDART suggested that selected hypothetical proteins of Vitis vinifera contain ATPase
family associated with various cellular activities (AAA) and belong to the AAA+ super family of ring-shaped P-loop containing
nucleoside triphosphate hydrolases. This study will lead to research in the optimization of the functionality of Rubisco which has
large implication in the improvement of plant productivity and resource use efficiency. |
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Keywords: | Rubisco activase Rubisco Vitis vinifera hypothetical protein homology modelling functional annotation |
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