RESEARCH HIGHLIGHTS - Characterisation and substrate binding modes of exopolygalacturonase PGQ1 from Saccharobesus litoralis

by Nor Azura Azami, Melissa Qianyue Lian, Go Furusawa & Aik-Hong Teh^∗

Pectin is a complex polysaccharide that constitutes a major component of terrestrial plant cell walls. It is composed of backbones of 1,4-linked α-D-galacturonate which are partially methylated and acetylated, and decorated by a variety of neutral sugars such as rhamnose, galactose, arabinose and xylose. Pectin degradation involves a combination of enzymes including pectin methylesterase, pectin acetylesterase, pectate lyase and polygalacturonase. Saccharobesus litoralis is capable of utilising pectin as well as agar, alginate and ulvan as carbon sources, with complete sets of the necessary genes encoded in its genome. S. litoralis harbours two polygalacturonases belonging to the glycoside hydrolase family 28 (GH28). One of them, PGQ1, cleaved polygalacturonate exolytically at the non-reducing end into monomeric units. It contained an elongated electropositive binding cleft made up of the catalytic triad Asp276, Asp297 and Asp298. In addition to the well conserved −1 and +1 subsites, docking analysis showed that PGQ1 might also accommodate a hexagalacturonate occupying up to the +5 subsite. Although Arg361 could bind to the sugar’s carboxyl group at the +3 subsite while Arg425 and Arg430 to that at the +5 subsite, interestingly no residues were available nearby to interact with the putative +2 and +4 subsites. Such a binding cleft with missing subsites, possibly a unique feature for the closely related GH28 exopolygalacturonases, might facilitate substrate transition into the −1 subsite for successive cleavage. The inability of S. litoralis to utilise extracellular galacturonate efficiently indicated that PGQ1, which harbours a Tat lipoprotein signal peptide, acted to degrade oligopectates in the periplasm. The new insights into PGQ1’s substrate binding may facilitate the engineering of improved polygalacturonases for industrial applications, such as the bioscouring of cotton fabrics and the generation of galacturonate as raw materials for biorefineries.




Link :  https://www.tandfonline.com/doi/full/10.1080/07391102.2023.2167111


CCB Ref.:  2023_RH_naa01
Date :  12/05/2023