Structure of a plant cell wall fragment complexed to pectate lyase C

The three-dimensional structure of a complex between the pectate lyase C (P elC) R218K mutant and a plant cell wall fragment has been determined by x-r ay diffraction techniques to a resolution of 2.2 Angstrom and refined to a crystallographic R factor of 18.6%, The oligosaccharide substrate, alpha-D- GalpA-([1-->4]-alpha-D-GalpA)(3)-(1-->4)-D-GalpA, is composed of five galac turonopyranose units (D-GalpA) linked by alpha-(1-->4) glycosidic bonds, Pe lC is secreted by the plant pathogen Erwinia chrysanthemi and degrades the pectate component of plant cell walls in soft rot diseases. The substrate h as been trapped in crystals by using the inactive R218K mutant. Four of the five saccharide units of the substrate are well ordered and represent an a tomic view of the pectate component in plant cell walls. The conformation o f the pectate fragment is a mix of 2(1) and 3(1) right-handed helices, The substrate binds in a cleft, interacting primarily with positively charged g roups: either lysine or arginine amino acids on PelC or the four Ca2+ ions found in the complex. The observed protein-oligosaccharide interactions pro vide a functional explanation for many of the invariant and conserved amino acids in the pectate lyase family of proteins. Because the R218K PelC-gala cturonopentaose complex represents an Intermediate in the reaction pathway, the structure also reveals important details regarding the enzymatic mecha nism. Notably, the results suggest that an arginine, which is invariant in the pectate lyase superfamily, is the amino acid that initiates proton abst raction during the beta elimination cleavage of polygalacturonic acid.