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Online Journal of Bioinformatics ©
Volume 13 (1):93-102, 2012
Homology model of sugarcane soluble acid invertase
Hemanthkumar M (PhD)1, Umamaheswari A (PhD)2
1Agricultural Research Station, ANGR Agricultural University, Perumallapalle, 2SVIMS Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati.
Hemanthkumar M, Umamaheswari A., Homology model of sugarcane soluble acid invertase, Online J Bioinform, 13 (1):93-102, 2012. Sucrose is a commercially important component of sugarcane (Saccharum spp.). The quality of sugarcane juice is determined by the concentration of sucrose. Invertases (α-fructofuranosidase) have been suggested to be key regulators for sucrose accumulation in sugarcane stem parenchyma and split sucrose into its glucose and fructose subunits by cleavage of α1-β2-glycosidic bond. Sucrose is lost during post harvest storage piling due to the continuous metabolic activity of living cells, microbial activity and endogenous soluble acid invertases. Homology modeling of sugarcane soluble acid invertase was performed. Soluble acid invertase protein sequence was retrieved from UniProt (O65342) and homologous performed through BLASTP analysis to reveal 3UGF as structural template (Identity: 59%). The homology model for protein was built using Modeller9v8 and structure was refined and validated through PROCHECK and ProQ. Results showed that 98.4% of the residues in the model fell in a favorable region of Ramachandran plot. An LGscore of 4.388 by ProQ analysis confirmed model accuracy and was posted at PDB with <3% stereo chemical check failure (PM0076107). The soluble acid invertase 3D structure model thus developed could be useful to design invertase inhibitors to prevent sucrose losses during sugarcane harvest.
Key words: Sugarcane soluble acid invertase, homology modeling, inhibitor designing.