Structural and sequence features of RWD Binding Domain (RWDBD).
a Structural model of yeast Gcn1 shown in two views obtained from fold recognition and homology modeling. b Representative alignment of the RWDBD domain family also showing the characteristic sequence motif ITGPLIR which is required for Gcn2 binding, generated using ESPript server (http://espript.ibcp.fr) . The columns shaded dark red show absolute conservation of residues and those shaded yellow show high conservation but contain minor substitution for residues which show highest proportion in the respective columns. The full alignment of this domain region is provided as HMM in Additional file 5. c Gcn1 along with the highly conserved and exposed residues are shown in brown shading. Most of the conserved and exposed residues are concentrated around Arg-2259, thus they can be potential protein-protein interface residues. d Electrostatic surface potential representation of Gcn1 homology model with the positive surface colored blue; negative surface colored red within the limits ± 10 kT/e. Arg-2259 of Gcn1 is located on the left side of the model and this surface is highly dominated by positive charge followed by a neutral region