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OJBTM
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.
ABSTRACT
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.