Molecular modeling of 2-nitropropane dioxygenase domain of Mycobacterium tuberculosis H37Rv and docking of herbal ligands.

The 3D structure of enoyl reductase (ER) domain generated by the SWISS MODEL server contains the 2-nitropropane dioxygenase (2NPD) structure displaying the TIM barrel fold. Though TIM barrel fold is made up of both main and inserted domains, in our study, we could only predict the structure of the main domain, which had central barrel of eight beta-strands surrounded by eight alpha-helices. Superimposition of the 2NPD region of ER domain of Mycobacterium tuberculosis H37Rv on to the corresponding region of 2UVA_G revealed a good structural alignment between the two, suggesting this template to be a good structural homologue.

Domain analysis of fatty acid synthase protein (NP_217040) from Mycobacterium tuberculosis H37Rv--a bioinformatics study.

Different domains of fatty acid synthase (FAS) protein of Mycobacterium tuberculosis H37Rv, involved in mycolic acid synthesis were analyzed using various bioinformatics tools. Based on different database searches (CDD and Pfam), FAS protein of Mycobacterium tuberculosis was grouped into eight domains, five of which showed close similarity with pdb templates (1MLA, 1IQ6A, 2BMOA, and 1J3NA). Based on the PSI blast analysis, 3D structures of only five domains were predicted using MODELLER software, and loop modeling was done for only those regions that were predicted as loops by predict protein server.