title: Molecular modeling of 2-nitropropane dioxygenase domain of Mycobacterium tuberculosis H37Rv and docking of herbal ligands.
abstract: 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. Among various herbal ligands that were screened as inhibitors, daucosterol was found to bind in closest proximity to the flavin mono nucleotide (FMN) binding site with the lowest docking energy.
authors.affiliation: Department of Biotechnology, Center for Postgraduate Studies, Jain University, 18/3, 9th Main, Jayanagar III Block, Bangalore 560011, India.
authors.forename: K V
authors.initials: KV
authors.lastname: Ramesh
authors.forename: B N
authors.initials: BN
authors.lastname: Akhila
authors.forename: Sudha
authors.initials: S
authors.lastname: Deshmukh
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D049308:Dioxygenases / Q000737:chemistry*; D050753:Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) / Q000737:chemistry*; D064429:Fatty Acid Synthases / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D016415:Sequence Alignment / Q000379:methods; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D049308:Dioxygenases; C021876:2-nitropropane dioxygenase; D050753:Enoyl-(Acyl-Carrier-Protein) Reductase (NADH); D064429:Fatty Acid Synthases