Figure 3

Assessment of the AtPSKR1 GC catalytic center by molecular docking of GTP. According to the 3D model of AtPSKR1, the GC domain is embedded within a cavity with the key residues for GTP interaction and the metal binding residue highlighted in yellow and cyan respectively. The GTP substrate docks successfully with the guanine portion at the inner-most of the cavity for interaction with the serine residue (position 1) and the phosphate end pointing outwards of the cavity towards the arginine residue (position 14) - an orientation deemed suitable for GC activity (A). When one or more key amino acid residues at position 1, 3 and/or 14 was replaced with leucine, docking experiments indicate disruptions in the docking orientations of GTP in all except for the leucine replacements at positions 1 and 3 of the GC domain. This suggests an aberrant GC catalytic activity when these key residues are replaced. GTP docking results for AtPSKR1 GC domain with leucine replacements at position 14 (B), positions 1 and 3 (C), and positions 1, 3 and 14 (D) are as illustrated. AtPSKR1-GCD (Asn⁸⁷¹ – Glu⁹⁸⁰) was modeled against the AvrPtoB-BAK1 complex (PDB entry: 3TL8) using the Modeller (ver. 9.10) software [14] while GTP docking experiments were performed using AutoDock Vina (ver. 1.1.2) [15]. The full-length AtPSKR1 protein and the domains organization are as shown in Additional file 2.