Homology modeling of family 39 glycoside hydrolase from Clostridium thermocellum

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 <0.005) and better sequence similarity. The phylogenetic tree showed that CtGH39 evolved from dockerin type cellulosome enzyme from Clostridium thermocellum ATCC 27405 and its closest neighbour is a hypothetical protein from Thermotoga petrophila. Multiple sequence alignment analysis of CtGH39 using MultAlin and HHpred showed above 90% similarities with protein sequences of Thermotoga petriphila (Hypothetical protein), Geobacillus stereothermophilus (1w91; 99.5%; E score=1.2 E-11), Thermoanaerobacterium saccharolyticum (1uhv; 99.4%; E score=2.9 E-11) and Bacillus stereothermophilus (1qw9; 98.5%; E score=4.9 E-6) from the PDB database. The secondary structure of CtGH39 using PSIPRED VIEW revealed many helices, strands and coils in the protein structure. The tertiary structure prediction of CtGH39 by MODELLER 8v2 showed a (ß/á)₈ fold. The program VERIFY 3D assessed the quality of the predicted structure of CtGH39 with acceptable scores. Ramachandran plot revealed that the structure of CtGH39 contains many segments of helix and further showed a tight grouping of phi (φ), psi (ψ) angles around -50, -50. There were 22 residues in 3₁₀ helical regions and 188 residues in beta sheets. The number of residues in alpha helix is 156 which are close to φ ~ -50 and ψ ~ -50 and these residues are clustered together. The Ramachandran plot for CtGH39 using RAMPAGE software showed that among 390 residues, 352 (90.7%) were in favoured region, 26 (6.7%) were in allowed region and 10 (2.6%) were in disallowed region elucidating the acceptability of the predicted model. All the results converged to the fact that the predicted 3-Dimensional structure of CtGH39 is of good quality with acceptable scores.