The discovery of a lactone isomerase involved in pectin degradation (LB137)

Abstract

Pectin, an abundant plant cell wall polymer, is being investigated as a possible raw material for the production of fuel and chemical products. To this end, an understanding of the steps to degrade pectin is useful. Agrobacterium tumefaciens strain C58 can use the primary constituent monomer of pectin, D‐galacturonate, as a sole carbon source and converts it to α‐ketoglutarate through a five step pathway in which the first step is oxidation of D‐galacturonate to D‐galactaro‐1,5‐lactone. We became interested in this pathway because a member of the functionally diverse enolase superfamily, designated Gci, catalyzes the third step in the pathway, and our lab has studied the enolase superfamily for over 20 years. We have identified an enzyme, D‐galactarolactone isomerase (GLI), adjacent to Gci in Agrobacterium’s genome, that catalyzes the second step in the pathway: the isomerization of D‐galactaro‐1,5‐lactone to D‐galactaro‐1,4‐lactone. The uncatalyzed isomerization reaction is “fast” and had been presumed to occur without the need of a catalyst. To characterize the enzyme‐catalyzed isomerization, we used 1H NMR to identify the activity, polarimetry to determine the kinetic constants (kcat = 440 s‐1, kcat/Km = 8.3 x 104 M‐1 s‐1, rate enhancement = 6.8 x 105), x‐ray crystallography to determine its structure, and gene expression analysis to connect the in vitro activity of the enzyme to an in vivo function. GLI is a member of the functionally diverse amidohydrolase superfamily and a homologue of LigI that catalyzes the hydrolysis of 2‐pyrone‐4,6‐dicarboxylate in lignin degradation. GLI’s ability to catalyze lactone isomerization instead of hydrolysis can be explained by the absence of the general basic catalysis used by LigI. This work identified the first example of lactone isomerization in the amidohydrolase superfamily and a missing enzyme in Agrobacterium’s pathway to catabolize pectin.Grant Funding Source: Supported by National Institutes of Health Grants P01GM071790 and U54GM093342 to J.A.G.