Structural Analyses of Substrate-pH Activity Pairing Observed across Diverse Polysaccharide Lyases

Area of Science:

• Biochemistry
• Enzymology
• Structural Biology

Background:

• Anionic polysaccharides and their degrading enzymes, polysaccharide lyases (PLs), exhibit significant functional and structural diversity.
• Structural convergence at the active sites of various PL folds suggests evolutionary adaptation for cleaving specific anionic polysaccharide classes.
• The role of extrinsic factors like pH in PL catalytic convergence, particularly concerning substrate binding and catalysis, remains incompletely understood.

Purpose of the Study:

• To investigate the functional convergence of polysaccharide lyases (PLs) concerning pH-dependent activity and substrate specificity.
• To determine the structural and computational basis for the conserved "substrate-pH activity pairing" observed across different PL families.
• To elucidate the key active site constituents responsible for pH-mediated catalytic activity in PLs.

Main Methods:

• Analysis of atomic superposition of various PL folds based on their cleavable substrate structures.
• Regrouping of PLs according to substrate type to analyze pH dependence of catalytic activity.
• Structural and computational definition of key active site constituents within and between PL families.

Main Results:

• Observed that specific substrate groups are cleaved within particular pH ranges (acidic, neutral, or basic), irrespective of the PL fold, supporting functional convergence.
• Identified conserved "substrate-pH activity pairing" across different PL families.
• Delineated the structural determinants responsible for this conserved pairing within PL active sites.

Conclusions:

• Functional convergence in PLs extends to pH-dependent activity, with distinct substrate classes being processed optimally at specific pH ranges.
• The study highlights the importance of pH as a critical factor influencing PL substrate specificity and catalytic efficiency.
• Structural determinants within PL active sites are key to understanding and predicting this conserved substrate-pH activity pairing.