Processive Pectin Methylesterases: The Role of Electrostatic Potential, Breathing Motions and Bond Cleavage in the Rectification of Brownian Motions
Figure 2
(A) Representation of the Ec-PME binding groove in an Ec-PME-HG decasaccharide complex. PME secondary structure is represented in cartoon and its surface is shown in white. The catalytic triad is represented in blue and coincides with the +1 subsite along the binding cleft. The HG decasaccharide is represented in cyan for carbon and red for oxygen atoms. (B) Electrostatic potential calculated for Ec-PME. The protein surface is colored in blue (positive) and red (negative) in the range between +3 kbT and −3 kbT (left panel). The negative patch observable in the active site is shown in close up (right panel) and is generated by the carboxylate groups of Asp178 and Asp199 that actively participate in the substrate catalysis and form an oxyanion. The oligosaccharide is shown, for clarity, in ball-and-stick representation and colored by atom type. Monosaccharide residues docked in the +1 and +2 subsites are labelled.
