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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.
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