DREB1A from Oryza sativa var. IR6: homology modelling and molecular docking

The family of AP2/ERF plant specific transcription factors, including dehydration-responsive element binding (DREB) proteins, has been reported to activate and bind with the dehydration responsive element/C repeat (DRE/CRT) of stress-inducible gene promoters. We amplified DREB1A from Oryza sativa var. IR6 (807 bp) and subjected it to protein homology modelling and phylogenetic analysis. BLAST sequence analysis indicated high similarity (99%) with the O. sativa japonica group. Phylogenetic analysis was carried out with other 12 DREB sequences from cereals/grasses using Clustal Omega. Protein secondary structure and 3D models were determined using SOPMA and MODELLER v9.10, respectively. PROSA was used to determine the excellence and consistency of models. The results indicated that the Z-score value was -2.94 and 79.5% of the residues were found in the favoured region. A psi/phi Ramachandran plot was determined using PROCHECK. The molecular docking of the GCC-box binding domain (GBD) of the protein under investigation was done using atomic coordinates of Arabidopsis thaliana GBD- and GCC-box containing DNA, respectively. The tertiary structure of the modelled protein and template were found to be very similar as predicted by a root mean square deviation of 0.968 angstrom. It seemed that both the proteins interacted with the major groove of DNA using beta-sheets. We attempted to expose the molecular basis of O. sativa var. IR6 DREB1A protein interaction with the target promoter sequence. The results highlighted that this gene could be a good candidate for production of abiotic stress-tolerant crop(s) in the future.