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Online Journal of Bioinformatics

Volume 5:129-131, 2004.

In silico gene identification and homology modeling of Chorismate synthase in Clostridium difficile.


Sunita T, Ramadevi S.


Informatics Division, GVK BIOSCIENCES Pvt Ltd, Hyderabad, India




Sunita T, Ramadevi S In silico gene identification and homology modeling of Chorismate synthase in Clostridium difficile Onl J Bioinform., 5 :129-131, 2004. Chorismate synthase (EC, catalyzes the last step in the common shikimate pathway leading to aromatic compounds. The shikimate pathway is absent in animals but present in bacteria, fungi, algae and parasites.  Chorismate synthase  is a potential therapeutic target for the rational design of novel antibacterials, antifungals, antiprotozoals, and herbicides. Herein is described the identification of gene for chorismate synthase in unfinished genome of Clostridium difficile, a gram positive bacteria involved in colitis and diarrhea. The predicted protein sequence has three conserved signature  patterns from regions rich in basic residues (mostly arginines) present in chorismate synthase of various species.  Homology modeling studies based on the crystal structure of chorismate synthase from Helicobacter pylori showed the conserved FMN binding site with two invariant histidine residues conserved in the active site : His(17) and His(106). The homology model described herein  should provide a structural framework on which the design of specific inhibitors may be based.


Keywords: aroC; chorismate synthase; FMN-binding protein; Clostridium difficile; shikimate pathway