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Comparative modeling of Undecaprenyl pyrophosphate phosphatase in Clostridium botulinum - a potent target of Botulism

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Author(s): Koteswara Reddy G. | Kaleswara Rao M. | Nagamalleswara Rao K. | Gyana R.Satpathy

Journal: International Journal of Systems Biology
ISSN 0975-2900

Volume: 2;
Issue: 2;
Start page: 10;
Date: 2010;
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Keywords: Clostridium botulinum F strain | comparative modeling | homology modeling | Ramachandran plot | Drug design

ABSTRACT
The bacteria Clostridium botulinum causing botulism. Botulism also known as botulinusintoxication is a rare but serious paralytic illness caused by botulinum toxin, which is produced by thebacterium Clostridium botulinum. Undecaprenyl pyrophosphate phosphatase is an enzyme, whichconsists in the sequestration of Undecaprenyl pyrophosphate. The enzyme function is to synthesize thecarrier lipid undecaprenyl phosphate that is essential for the biosynthesis of peptidoglycan and other cellwall components in Clostridium botulinum. The objective of enzyme inhibition needs structuralcharacterization from its 3-D structure in rational structure based drug design. Homology modeling canproduce high-quality structural models when the target and templates are closely related. MODELLER isthe program used for homology modeling which provides accurate and efficient models to build loopsand side chains found non-identical in sequence. It implements comparative protein structure modelingby satisfaction of spatial restraints. The stereo chemical quality of a best model is validated byPROCHECK server with 86.2% residues under favored region from Ramachandran plot. The CASTp isused for locating, delineating and measuring concave surface regions on three-dimensional structures ofproteins. The residues are identified in burial cavity of the best model as Tyr (66), Lys (69, 75, 86), Ile(70,101,106,186), Asn (76), Ser (72,100), Phe (78), Pro (102), Ala (103), Val (187), and Leu (189) withhydrophobic nature. These include pocket located on protein surfaces and voids buried in the interior ofproteins that are frequently associated with binding events. Thus present studies of modeling ofUndecaprenyl pyrophosphate phosphatase enzyme has brought future prospective to fight againstbotulism disease and provide better health standaaards for community.
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