Homology modeling of the central catalytic domain of insertion sequence ISLC3 isolated from Lactobacillus casei ATCC 393

Abstract

The tertiary structure of the central catalytic domain of insertion sequence ISLC3 isolated from Lactobacillus casei ATCC 393 was predicted using the homology modeling approach. The novel insertion sequence was isolated by us from the template bacteriophage phiA3 of L.casei ATCC 393. The number of amino acid residues of the ISLC3 central catalytic domain was 116 and was treated as the query sequence. There were five Web-available threading methods used to find some primary structure templates for the query sequence. These primary templates were further screened using the SWISS-MODEL Protein Modeling Server and the default parameter settings therein to give six final structure templates. All of these final structure templates were the integrase (IN) protein of retroviruses. Multiple sequence alignment using these IN sequences against the query one revealed the signature DDE motif. Based on the structures of these final templates, the structure of the query sequence was constructed using the InsightII/Discover/Homology programs. A metal ion, Mg(2+), was inserted into the center of the putative catalytic pocket formed by the DDE residues of the predicted structure in the final rounds of refinement by molecular dynamics (MD) simulations. The structure with a metal ion included was designated with Mg and that without a metal ion was designated free Mg. The average exposed surface area of some hydrophobic residues of both the predicted free Mg and with Mg structures were computed and compared with those computed for the six structure templates. Whereas the predicted with Mg structure was slightly more exposed than the predicted free Mg structure, the former appeared to be more stable than the latter, as revealed by the lower conformation energy recorded for the former during the structure refinement by MD simulations. To verify further the predicted structures, the coordinates of both predicted structures were fed into the ERRAT Protein Verification Server. It was found that the quality of the predicted with Mg structure was much better than that of the free Mg structure. The validation results also indicated that regions of the predicted with Mg structure that can be rejected at the 95% confidence level were approximately 20% whereas those which can be rejected at the same level for the six structure templates were approximately 10%. The predicted with Mg structure was also docked into a short oligonucleotide representing the substrate of the ISLC3 transposase using the DOCK_4.0.2 program. It was found that both Glu140 and Asp68 residues of the DDE motif of the predicted with Mg structure were able to form hydrogen bonds with the DNA substrate, which was similar to what was observed in a docking study using the retrovirus IN 1asu and its DNA substrate.