title: Sequence and 3D structure based analysis of TNT degrading proteins in Arabidopsis thaliana.
abstract: TNT, accidentally released at several manufacturing sites, contaminates ground water and soil. It has a toxic effect to algae and invertebrate, and chronic exposure to TNT also causes harmful effects to human. On the other hand, many plants including Arabidopsis thaliana have the ability to metabolize TNT either completely or at least to a reduced less toxic form. In A. thaliana, the enzyme UDP glucosyltransferase (UDPGT) can further conjugate the reduced forms 2-HADNT and 4-HADNT (2-hydroxylamino-4, 6- dinitrotoluene and 4-hydroxylamino-2, 6- dinitrotoluene) of TNT. Based on the experimental analysis, existing literature and phylogenetic analysis, it is evident that among 107 UDPGT proteins only six are involved in the TNT degrading process. A total of 13 UDPGT proteins including five of these TNT degrading proteins fall within the same group of phylogeny. Thus, these 13 UDPGT proteins have been classified into two groups, TNT-degrading and TNT-non-degrading proteins. To understand the differences in TNT-degrading capacities; using homology modeling we first predicted two structures, taking one representative sequence from both the groups. Next, we performed molecular docking of the modeled structure and TNT reduced form 2-hydroxylamino-4, 6- dinitrotoluene (2-HADNT). We observed that while the Trp residue located within the active site region of the TNT- degrading protein showed π-Cation interaction; such type of interaction was absent in TNT-non-degrading protein, as the respective Trp residue lay outside of the pocket in this case. We observed the conservation of this π-Cation interaction during MD simulation of TNT-degrading protein. Thus, the position and the orientation of the active site residue Trp could explain the presence and absence of TNT-degrading capacity of the UDPGT proteins.
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata, 700009, India.
authors.forename: Amrita
authors.initials: A
authors.lastname: Bhattacherjee
authors.forename: Rahul Shubhra
authors.initials: RS
authors.lastname: Mandal
authors.forename: Santasabuj
authors.initials: S
authors.lastname: Das
authors.forename: Sudip
authors.initials: S
authors.lastname: Kundu
mesh_terms: D000814:Aniline Compounds / Q000737:chemistry / Q000378:metabolism; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001711:Biotransformation; D004136:Dinitrobenzenes / Q000737:chemistry / Q000378:metabolism; D014453:Glucuronosyltransferase / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D014303:Trinitrotoluene / Q000737:chemistry* / Q000378:metabolism; D014530:Uridine Diphosphate / Q000378:metabolism
chemical_list: D000814:Aniline Compounds; D029681:Arabidopsis Proteins; D004136:Dinitrobenzenes; D014303:Trinitrotoluene; D014530:Uridine Diphosphate; C085951:4-hydroxylamino-2,6-dinitrotoluene; D014453:Glucuronosyltransferase