Figure 6. Model of substrate bound SHIP2.

(A) The SHIP2 Ptase-PI(3,4,5)P₃-diC8 complex is modeled based on crystal structures of the homologue INPP5B crystal structure bound to PI(4)P (pdbs: 3MTC). L4 is in the ‘in’ conformation and R682 makes hydrogen bonds to the PI(3,4,5)P₃ 3-phosphate (P3). N540 and K541 interact with P1, N684 and Y661 with P4, H718 with P5 and L2 with PI(3,4,5)P₃ lipid chains. The attacking water, bound to D607, is colored light blue and the Mg²⁺ ion is shown as green sphere. (B) Close-up of the Mg²⁺ coordination. (C–D) Plotted are RMSDs of the substrate headgroup atoms compared to the starting positions during MD simulations of the SHIP2 Ptase or Ptase-C2 bound to IP₄ (C) or PI(3,4,5)P₃-diC8 (D). The simulations are started with substrate positions according to the model shown in panel (A).

DOI: http://dx.doi.org/10.7554/eLife.26640.020

Figure 6—figure supplement 1. Structure of Ptase-C2 D607A, crystallized in presence of PI(3,4,5)P₃-diC8 and Mg²⁺.

(A) Electron density for one Mg²⁺ and one phosphate group is clearly visible in 6 of the eight molecules (shown is molecule H). 2Fo-Fc electron density is shown in blue countered at a σ level of 1.0. (B) Superposition of our model of the SHIP2 Ptase bound to PI(3,4,5)P₃ and Mg²⁺ in the Michaelis-Menten complex (tan) with the 6 Ptase-C2 D607A molecules bound to Mg²⁺ and phosphate (green; only Mg²⁺ as small crosses and phosphates are shown), the Mg²⁺ and phosphate bound INPP5B structure (cyan, pdb: 5A7I) and the two-metal bound APE1 structure (grey, pdb: 1E9N). The E473 and D607 side chains labeling corresponds to SHIP2 numbering and the A- and B-metal sites in the APE1 structure are indicated.

DOI: http://dx.doi.org/10.7554/eLife.26640.021