PelQ1 from Saccharobesus litoralis is a Ca2+-dependent pectate lyase belonging to the polysaccharide lyase family 1 (PL1). Although being an endolytic enzyme, it degraded polygalacturonate into predominantly unsaturated trimer in an exolytic manner with delayed production of dimer, tetramer and pentamer. The enzyme harbours a C-terminal domain from the carbohydrate-binding module family 13 (CBM13), whose presence facilitated the production of dimer. PelQ1's homology model showed that it possessed a well-conserved catalytic cleft, with R232 acting as the general base and R203 as the general acid. Structural comparison with DcPelC, a similar trimer-generating pectate lyase from Dickeya chrysanthemi EC16, implied that both enzymes' catalytic clefts encompassed at least eight subsites, i.e. -5 to +3. The unequal distribution of the subsites between the reducing and non-reducing ends of the cleavage site might be responsible for the exolytic generation of the trimer. As all but the -1, +1 and + 2 subsites could accommodate methylated galacturonate, this subclass of PL1 pectate lyases may function to help break up methylated pectin.
Yeast cell death is triggered when essential nutrients such as potassium and lipid are limited but ammonium is in excess. When ammonium and glucose were maintained at 100% of the normal concentration while all the other essential nutrients in yeast nitrogen base (YNB) were reduced to 2%, yeast growth was halted by ammonium toxicity. Yeast started to grow again when either ammonium was also reduced to 2% or gluconate was added, but simultaneously adding gluconate as well as reducing all the nutrients except glucose 50-fold revived yeast growth to a greater extent, i.e. a quarter of the normal growth. Gluconate, as well as formate and alginate, stimulated yeast growth by buffering the drop in pH. Yeast cells were seemingly more susceptible to low pH under the nutrient-limited conditions, entering the stationary phase at pH higher than that of the normal condition. Carboxylate salts may prove a cost-efficient replacement for large proportions of the essential nutrients as yeast cells, in the presence of 2 mg ml-1 gluconate, could still achieve nearly 90% of the normal growth when cultured in only 10% of the normal YNB concentration.
Among the enzymes required for the efficient utilisation of pectin is polygalacturonase. Saccharobesus litoralis harbours two polygalacturonases belonging to glycoside hydrolase family 28 (GH28). One of them, PGQ1, cleaved polygalacturonate exolytically at the non-reducing end into monomeric units. It was most active at 60 °C and pH 8, with Km and kcat values of 2.3 mg/ml and 6.4 s-1 respectively. Its homology model of a right-handed parallel β-helix core consisted of Asp297 as the general acid and either Asp276 or Asp298 as the general base. By inferring the substrate binding modes at the -1 and +1 subsites from known crystal structures, a hexagalacturonate could be docked into the highly electropositive binding cleft. Interestingly, while no residues were present in the vicinity to make up the +2 and +4 subsites, Arg361 and Arg430 could readily bind to the carboxyl groups of the galacturonates at the +3 and +5 subsites respectively. Structural comparison suggested that this binding pattern with missing subsites might be unique to closely related exopolygalacturonases. As S. litoralis grew much more slowly on extracellular galacturonate due to the lack of a transporter for the monosaccharide, PGQ1 probably functioned in the periplasm to help degrade oligopectates completely.Communicated by Ramaswamy H. Sarma.