THREE DIMENSIONAL STRUCTURE PREDICTION AND IN SILICO FUNCTIONAL ANALYSIS OF GAMMA TOCOPHEROL METHYL TRANSFERASE FROM Glycine max

T. VINUTHA¹, N. BANSAL², G.R. PRASHAT³, V. KRISHNAN⁴, S. KUMARI⁵, A. DAHUJA⁶, A. SACHDEV⁷, R.D. RAI^8
1Division of Biochemistry, Indian Agricultural Research Institute, New Delhi- 110 012, India.
²Division of Biochemistry, Indian Agricultural Research Institute, New Delhi- 110 012, India.
³Division of Genetics, Indian Agricultural Research Institute, New Delhi- 110 012, India.
⁴Division of Biochemistry, Indian Agricultural Research Institute, New Delhi- 110 012, India.
⁵Division of Biochemistry, Indian Agricultural Research Institute, New Delhi- 110 012, India.
⁶Division of Biochemistry, Indian Agricultural Research Institute, New Delhi- 110 012, India.
⁷Division of Biochemistry, Indian Agricultural Research Institute, New Delhi- 110 012, India.
⁸Division of Biochemistry, Indian Agricultural Research Institute, New Delhi- 110 012, India.

Received : 03-11-2014     Accepted : 01-01-2015     Published : 02-06-2015
Volume : 6     Issue : 1       Pages : 294 - 304
Int J Bioinformatics Res 6.1 (2015):294-304

Keywords : Glycine max, γ-TMT, secondary structure, ligand binding site, SAM, Motif
Conflict of Interest : None declared

γ-Tocopherol methyl transferase (γ-TMT) involved in synthesis of tocopherol (vitamin-E) methylates γ- and δ- tocopherols to form α- and β-tocopherols respectively. γ-TMT of soybean (Glycine max L.) was found to be a water soluble protein with the highest amount of polar amino acids contributing to its molecular surface hydrophilicity; the protein was found to be highly thermostable with half-life of < 5hr under in-vivo conditions. The isoelecric point (6.3) of the protein rendered the protein activity in the acidic buffer. We predicted three dimensional structure of γ-TMT as a monomer harboring majority of the α-helical structures and with the highest amount of hydrogen-bonded turns and extended strands in the β-ladder. Qualitative and quantitative analyses of the resulting model suggested the proposed model to be reliable with MPQS value of 1.24, an estimated native overlap at 3.5A0 of about 72.5%, a discrete optimized protein energy of - 0.48 and with a Z-score of 51.10. The predicted model was found to be stable taking into consideration more than 94.1% of the residues in the most favored regions. The structural superimposition of the predicted structure indicated a highly conserved structure despite its low amino acid similarity with the template protein. The results also led to the identification of the functional SAM/SAH binding sites such as HIS38, HIS40, GLY88 and ILE111 on γ-TMT and revealed the presence of the largest cleft on the surface which may play a major role during the ligand-protein interactions. Phylogenetic tree analysis revealed the Glycine max γ-TMT to be evolutionarily modified from photosynthetic bacterial MPBQ methyl transferase. Thus the predicted three dimensional structure and other related information generated in the present study have potential implications in better understanding of the molecular mechanisms and nature of methyl transferase related enzymatic reactions.