Pectin is a polymeric material havi

Pectin is a polymeric material having carboxylic groups esterified with methanol. It can be divided in two regions ‘‘smooth region’’ and ‘‘hairy region’’ [Fig. 2]. The degree of esterifications varies depending on its source. It mostly consist of three structurally well-characterized polysaccharide motifs: homogalacturonan (HGA), rhamnogalacturonan I and rhamnogalacturonan II (RG I and RG II) [12,13]. These three polysaccharides form a network, which has a considerable potential for modulation of its structures by action of cell wall degrading enzymes. Homogalacturonan represents the backbone chain of the pectin molecule, containing a-1,4-linked residues of D-galacturonic acid, which can be methylated at the O-6 position. RG I is located in the highly branched area containing large number of side chains of a-1,2-linked residues of L-rahmnopyranose whereas the more complex RG II structure has been identified in the primary cell wall of some plants [14]. It is believed to play a role as a signal molecule in plant cell wall development rather than being a structural polymer [15]. The pectin molecule is branched at the rhamnogalacturonan part by side chains like arabinans, galactans or arabinogalactans which are linked by b-(1,4) linkages to rhamnose. In the main side chains, the arabinose units are a-(1–5) linked and the galactose units are joined by b-(1–4) linkages. Apart from these neutral sugars, the side chains of pectins can also contain xylopyranose, D-glucopyranose and L-fucopyranose, whereas in RG II, D-apiose, 2-O-methyl-D-xylose and 2-Omethyl-L-fucose are present. In RG I the galacturonic acid residues are often acetylated at the C2 or C3 position, but acetylation was found also in the homogalacturonan region. Generally, pectins have variable compositions [16]. D-Galacturonic acid residues form most of the molecules in blocks of ‘smooth’ and ‘hairy’ regions. The molecule does not adopt a straight conformation in solution but is extended and curved (worm-like) with a large amount of flexibility. The ‘hairy’ regions of pectins are even more flexible and may have pendant arabinogalactans. The carboxylate groups tend to expand the structure of pectins as a result of their charge unless they interact through divalent cationic bridging (their pKas are of about 2.9) ensuring considerable negative charge under most circumstances [17]. Methylation of these carboxylic acid groups forms their methyl esters, which take up a similar space but are much more hydrophobic and consequently have a different effect on the structuring of the surrounding water. The properties of pectins depend on the degree of esterification, which is normally about 70%.
Since considerable variability in the composition of pectins from different sources have been observed, it follows that the kinetic characteristics like Km and kcat for pectin lyases should also depend on the pectin used for the studies. By the studies of mode of action of pectin lyase A of Aspergillus niger on differently C6 substituted ologogalacturonides it has been concluded that pectin lyase A is very specific for highly esterified pectins, removal of ester groups or changing the type of ester resulted in the complete loss of activity [18]. However increasing the esterification of pectin increases the activity of pectin lyase A.
3. Enzymes related to pectin lyases
There is a group of pectinolytic enzymes broadly known as pectinases which are involved in pectin degradation. These enzymes have been reviewed a number of times. Based on mode of action and preferred substrate these enzymes can be briefly classified as mentioned below [Table 1]. Due to the great diversity in the structure of pectins they can be categorized into enzymes acting on the ‘‘smooth regions’’ composed of homogalacturonan and enzymes acting on the ‘‘hairy region’’ composed of rhamnogalacturonan and side chains. The groups of enzymes which are involved in the degradation of hairy region of pectins are rhamnogalacturonan hydrolase (RG hydrolase), rhamnogalacturonan lyase, rhamnogalacturonan rhamnohydrolase (RG rhamnohydrolase), rhamnogalacturonan galactohydrolase (RG galactouronohydrolase). These enzymes have rarely been studied [19–22] and need extensive studies on their structures and functions. There are however other accessory enzymes involved in degradation of side chains of pectins