April Journal-2009.p65 - Association of Biotechnology and Pharmacy

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Current Trends in Biotechnology and Pharmacy Vol. 3 (2) 210-218, April 2009. ISSN 0973-8916 Homology modeling of family 39 glycoside hydrolase from Clostridium thermocellum Shadab Ahmed, Tushar Saraf and Arun Goyal* Department of Biotechnology, Indian Institute of Technology Guwahati Guwahati-781039, Assam, India * For correspondence - arungoyl@iitg.ernet.in Abstract The homology based 3-Dimensioanl structure prediction of family 39 glycoside hydrolase (CtGH39) from Clostridium thermocellum was carried out using bioinformatics tools. The Ctgh39 gene from Clostridium thermocellum is 1170 base pair sequence. The CtGH39 sequence on PSI-BLAST analysis for homology search revealed 54 hits and out which a few had significant E score (E
Current Trends in Biotechnology and Pharmacy Vol. 3 (2) 210-218, April 2009. ISSN 0973-8916 211 contributing to the carbon cycle and the natural decomposition of biomass. Biodegradation and carbon cycle impact the environment because nutrients and more usable compounds are available for other organisms to feed on. This bacterium degrades the cellulosic materials by a large multi-enzymes system called the “cellulosome”. The cellulosome is a complicated protein complex consisting of nearly 20 different catalytic subunits or glycoside hydrolases ranging in size from about 40 to 180 kDa with a total molecular weight in millions. The database for glycoside hydrolases is available at website (http:/ /www.cazy.org/fam/acc_GH.html) (2), that contains classification of glycoside hydrolases in the families based on amino acid sequence similarities: i) reflects the structural features of these enzymes ii) helps to reveal the evolutionary relationships between these enzymes iii) provides a convenient tool to derive mechanistic information. According to the glycoside hydrolase classification system, several families GH3, GH39 and GH43 exhibit â-xylosidase activity (3,4,5,6,7). The IUBMB enzyme nomenclature of glycoside hydrolases is based on their substrate specificity and occasionally on their molecular mechanism; such a classification does not reflect the structural features of these enzymes. Family 39 glycoside hydrolases (EC:3.2.1.—) are group of enzymes that hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. The known activities of GH39 are: i) á-L-iduronidase (EC:3.2.1.76) and ii) â-xylosidase (EC:3.2.1.37). In most cases, the hydrolysis of the glycosidic bond is performed by two catalytic residues of the enzyme vis-a-vis a general acid residue (proton donor) and a basic residue. Depending on the spatial position of these catalytic residues, hydrolysis occurs via overall retention of the anomeric configuration (8). MODELLER is used for homology and comparative modelling of protein threedimensional structures (9,10). MODELLER implements comparative protein structure modelling by satisfaction of spatial restraints (11,12). It can perform many additional tasks, including de novo modelling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignments of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures. G.N. Ramachandran used computer models of small polypeptides to systematically vary phi and ψ with the objective of finding stable conformations (13). For each conformation, the structure was examined for close contacts between atoms. Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii. Therefore, φ and ø angles which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone. In a Ramachandran plot (13), the core or allowed regions are the areas in the plot show the preferred regions for psi/phi angle pairs for residues in a protein (14). Presumably, if the determination of protein structure is reliable, most pairs will be in the favoured regions of the plot and only a few will be in “disallowed” regions. (14,15). Extensive scientific work on C. thermocellum has been done on the genes that control cellulose degradation. Over 100 genes are involved in encoding proteins involved in cellulose degradation. This research is essential for future development of conversion of biomass into energy that can be achieved by understanding the genes encoding the cellulose degrading proteins and how their expressions are regulated. Cellulose degrading ability of C. thermocellum can be manipulated and amplified as a mass energy source. In the present study the sequence analysis and homology based 3- dimensioanl structure prediction of family 39 glycoside hydrolase (CtGH39) from Clostridium thermocellum using above bioinformatics tools Ahmed et al
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April Journal-2009.p65 - Association of Biotechnology and Pharmacy

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