Fig. 6
From: Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site
Displacement pathway of Glc, based on crystal structures and molecular modelling. a Converged HvExoI:Glc:G3OG complex obtained by docking. Selected residues (carbons: atomic and purple sticks), Glc (carbons: yellow sticks) and G3OG (carbons: orange sticks) are shown. Glc in the −1 subsite is separated from the lateral cavity by the Arg158-Glu491-Asp285 (carbons: purple sticks) toll-like barrier (dashed lines). Surface morphology coloured by electrostatic potentials: white, neutral; blue, +5 kT e−1; red, −5 kT e−1. b Glc cannot exit, when crystallographic coordinates are considered by GaudiMM (grey symbols). Glc displacement only occurs when protein atoms are relocated to the lowest-energy normal mode (black). Clashes of Glc are shown as the function of separations from the Glc geometric centre in the −1 subsite. Displacement routes present fewer clashes, when MD structures are considered (green) and protein atoms move (dark red). c Lowest-energy normal mode shows a cork-like motion of domains 1 and 2. d Glc displacement routes calculated by PELE using ternary HvExoI:Glc:substrate complexes 1–3. PELE binding energies, plotted as a function of Glc separation from the −1 subsite, show that Glc traverses via the lateral cavity at the separation of 8 Å from protein surface. Full, semi-dashed, dashed and dotted lines specify separation ranges of 2–3 Å, 5–7 Å, 8–11 Å and 13–17 Å (referring to line thickness in (e–h)) between respective centres of masses and C4-OH groups of Glc in initial and final structures. e–h Four steps along the Glc displacement route based on complexes 1–3 (Glc carbons: yellow spheres). Left and right images are rotated by 200o (e–g) and −50o (h) along y-axes. e Glc is in the −1 subsite. f Movements of Arg158, Asp285 and Glu491 allow Glc traversing into the lateral cavity. g Glc in the lateral cavity is partly exposed to the bulk solvent. h Glc is fully exposed to the bulk solvent. Black dotted ellipsoid indicates the transient solvent-exposed aperture of the lateral cavity that facilitates Glc displacement
