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Accuracy of the best obtained models, calculated as coordinate root-mean-square deviation (cRMSD) between the target and the modeled structures, was under 1 Å, which is competitive with experimental methods, such as crystallography or NMR.

Structure refinement of modeled structures was carried out using the Discovery Studio software suite version 3.0 (Accelrys Inc , USA.

The stereochemical quality of the modeled structures was verified using the PROCHECK 25 and WHAT_CHECK 26 algorithms and by assessment of Ramachandran plots.

Finally, the feasibility of modeled structures was evaluated by Verify3D to ensure that all the predicted structures had an acceptable 3D-1D self-compatibility score.

The only significant difference between the modeled structures was the inverted ribose conformation of the two substrates to maintain the correct geometry of their 5′-OH groups for phosphoryl transfer.

Finally, the CHARMM based Energy minimization of the modeled structures was performed to remove steric overlaps that cause bad contacts; the initial potential energies of starting structures and the potential energy of respective minimized structures are given in Additional file 6.

Structural constraints and prediction quality of the modeled structures were evaluated using WHATIF [ 35] and PROCHECK [ 36].

Modeled structures were subjected to energy minimization and final models presented high-quality local and overall stereochemistry with approximately 98% of amino acid residues lying in allowed regions of the Ramachandran plot.

All the calculations of modeled structures were carried out for 300 K.

Verify_3D showed that the overall scores of the modeled structures were greater than 85 indicating a good compatibility between the 3-D modeled structure and its corresponding 1-D amino acid sequence.

The modeled structures were then re-minimized.