Homology modeling of family 39 glycoside hydrolase from Clostridium thermocellum

Order of Publishing in Issue: 
12
Volume :3
Issue :2
April, 2009
Page No: 
210-218
Authors: 
Shadab Ahmed, Tushar Saraf and Arun Goyal*
Address: 
Department of Biotechnology, Indian Institute of Technology Guwahati Guwahati-781039, Assam, India

AbstractThe homology based 3-Dimensioanlstructure prediction of family 39 glycosidehydrolase (CtGH39) from Clostridiumthermocellum was carried out usingbioinformatics tools. The Ctgh39 gene fromClostridium thermocellum is 1170 base pairsequence. The CtGH39 sequence on PSI-BLASTanalysis for homology search revealed 54 hits andout which a few had significant E score (E <0.005)and better sequence similarity. The phylogenetictree showed that CtGH39 evolved from dockerintype cellulosome enzyme from Clostridiumthermocellum ATCC 27405 and its closestneighbour is a hypothetical protein fromThermotoga petrophila. Multiple sequencealignment analysis of CtGH39 using MultAlin andHHpred showed above 90% similarities withprotein sequences of Thermotoga petriphila(Hypothetical protein), Geobacillusstereothermophilus (1w91; 99.5%; E score=1.2E-11), Thermoanaerobacterium saccharolyticum(1uhv; 99.4%; E score=2.9 E-11) andBacillus stereothermophilus (1qw9; 98.5%; Escore=4.9 E-6) from the PDB database. Thesecondary structure of CtGH39 using PSIPREDVIEW revealed many helices, strands and coilsin the protein structure. The tertiary structureprediction of CtGH39 by MODELLER 8v2showed a (ß/á)8 fold. The program VERIFY 3D
assessed the quality of the predicted structure ofCtGH39 with acceptable scores. Ramachandranplot revealed that the structure of CtGH39contains many segments of helix and furthershowed a tight grouping of phi (?), psi (?)angles around -50, -50. There were 22 residuesin 310 helical regions and 188 residues in betasheets. The number of residues in alpha helix is156 which are close to ? ~ -50 and ? ~ -50 andthese residues are clustered together. TheRamachandran plot for CtGH39 usingRAMPAGE software showed that among 390residues, 352 (90.7%) were in favoured region,26 (6.7%) were in allowed region and 10 (2.6%)were in disallowed region elucidating theacceptability of the predicted model. All the resultsconverged to the fact that the predicted 3-Dimensional structure of CtGH39 is of goodquality with acceptable scores.

Keywords: 
Homology modeling of family 39 glycoside hydrolase from Clostridium thermocellum
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