Structural analyses of ‘substrate-pH of activity’ pairing observed in Polysaccharide lyases

Abstract

AbstractAnionic polysaccharides found in nature are functionally and structurally diverse, and so are the polysaccharide lyases (PLs) which catalyse their degradation. Atomic superposition of various PL folds according to their cleavable substrate structure confirm the occurrence of structural convergence at PL active sites. This suggests that various PL folds have emerged to cleave a particular class of anionic polysaccharide during the course of evolution. While structural and mechanistic similarity of PLs active site have been highlighted in earlier studies, a detailed understanding regarding functional properties of this catalytic convergence remains an open question, especially the role of extrinsic factors such as pH in the context of substrate binding and catalysis. Our earlier structural and functional work on pH directed multi-substrate specificity of Smlt1473 inspired us to regroup PLs according to substrate type to analyse the pH dependence of their catalytic activity. Interestingly, we find that particular groups of substrates are cleaved in a particular pH range (acidic/neutral/basic) irrespective of PLs fold, boosting the idea of functional convergence as well. Based on this observation, we set out to define structurally and computationally the key constituents of an active site among PL families. This study delineates the structural determinants of conserved ‘substrate-pH activity pairing’ within and between PL families.