Polysaccharide lyase

Akita, M., Suzuki, A., Kobayashi, T., Ito, S., and Yamane, T. (2001). The first structure of pectate lyase belonging to polysaccharide lyase family 3. Acta CrystaUogr. D Biol. Crystalhgr. 57, 1786-1792. 

Rye, C. S. Withers, S. G., The synthesis of a novel thio-linked disaccharide of chondroitin as a potential inhibitor of polysaccharide lyases. Carbohydr. Res. 2004, 339, 699-703. 

Charnock, S.-J. et al. (2002). Convergent evolution sheds light on the anti-jS-ehmination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Science, USA, 99, 12067-72. 

Polysaccharide Lyases. The results on the modification of 4-0-methylglucuronic acid indicate that C5 epimerisation and elimination of 04 are comparably facile processes in vitro. Natural selection therefore predicts that where enzymes have evolved in the same organism, working on the same substrate, to perform both epimerisation and elimination, they should be structurally and evolutionarily related. A case in point is the alginate lyases and epimerases, although the sequences of modern lyases and epimerases are not similar, possibly because of the different stereochemical requirements of the... 

Although most polysaccharide lyases and epimerases act on the polyuronic acids, a number of those acting on pectin do so on the methyl esters. Whereas the second pifa of acetic acid is around 35-36, the of ethyl acetate is 25, ... 

Polysaccharide lyases have been grouped into a number of CAZy families and mechanistic and structural data are available for a number of them. As with the glycoside hydrolases, enzymes of the same CAZy family have the same protein fold and similar, if not identical, mechanisms. In June 2007 there were 18 polysaccharide lyase families. 

Polysaccharide lyase Family 8 (PL 8). This family encompasses lyases acting upon mammalian connective tissue glycosaminoglycans, and for this reason is the best investigated, with a number of crystal structures available. It has a two-domain fold with an (a/ot)5 toroid connected to a domain almost exclusively of (3-sheet. The reactions catalysed are syn eliminations, with available evidence indicating an irreversible 1cb mechanism, in which the intermediate enolate is stabilised by hydrogen bonding, rather than metal ions, and both deprotonation of C5 and protonation of 04 are carried out by the same tyrosine residue. 

The Linhardt laboratory prepares polysaccharide lyases from Flavobacterium heparinum and Bacteroides stearcoris. These enzymes have been purified to homogeneity, cloned, and expressed in bacteria. Their physical and catalytic properties and specificity have been extensively investigated. ... 

Table 2. Properties of polysaccharide lyases acting on glycosaminoglycans...

Polysaccharide lyases have been used to produce A -uronate containing disaccharides (Figure 4, la-lr) and higher oligosaccharides from heparin, heparan sulfate, chondroitin sulfates, dermatan sulfate, hyaluronan, and chemically modified GAGs. ... 

Polysaccharide lyases can be combined with separation methods such as chromatography and electrophoresis for the preparation of glycosaminoglycan oligosaccharides for biological evaluations as well as for disaccharide analysis, oligosaccharide mapping and polysaccharide sequencing. 

As with glycoside hydrolases, the polysaccharide lyases (PL) have long been classified into sequence-related protein families (129) in the CAZy database (28). Presently, more than 20 PL families are listed in CAZy, and, because of significant recent attention, at least one three-dimensional structural representative is known for approximately one half of these (reviewed in Refe. (126,127), and (130) see also http //www.cazy.org/fam/acc PL.html). Not surprisingly, these endo-acting enzymes possess cleft-shaped active sites (126), akin to the polysaccharide erac/o-glycosidases vide supra). Characteristically, polysaccharide lyases bind their polyanionic substrates through basic amino acid residues and/or Ca++ ion complexation. Indeed, the activity of nearly all known pectate lyases strictly requires Ca++, which in some cases may directly affect the catalysis (126). 

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