Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
Polysaccharide lyases (PLs) have been assigned to 21 families based on their sequences, with ~ 50 singletons awaiting further classification. For 19 of these families, the structure of at least one protein is known. In this review, we have analyzed the available structural information and show that presently known PL families belong to six general folds. Only two general catalytic mechanisms have been observed among these PLs: (1) metal-assisted neutralization of the acidic group of the sugar next to the cleaved bond, with, rather unusually, arginine or lysine playing the role of Brønsted base and (2) neutralization of the acidic group on the sugar by a close approach of an amino or acidic group forcing its protonation and Tyr or Tyr-His acting as the Brønsted base and acid.
Garron
Marie-Line
ML
Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6.
Cygler
Miroslaw
M
D000818:Animals; D002384:Catalysis; D006801:Humans; D011133:Polysaccharide-Lyases / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D014574:Uronic Acids / Q000737:chemistry / Q000378:metabolism
D014574:Uronic Acids; D011133:Polysaccharide-Lyases