Elucidating the catalytic mechanism of a bacterial deglycase essential for utilization of fructose‐lysine, an Amadori product

Amadori products are stable sugar-amino acid conjugates that are formed non-enzymatically via the Maillard reaction that takes place during preparation of foods by heating, roasting, and drying. Fructose-lysine (F-Lys, ε-conjugated) is one of the most abundant Amadori compounds in processed foods and is a key intermediate in the formation of advanced glycation end products, which in turn are implicated in inflammation and disease. The variation among humans in their ability to metabolize F-Lys has motivated an examination of the inter-individual differences in gut microbial taxa and the enzymes that help convert F-Lys into short-chain fatty acids or cellular energy. Results from such studies are also expected to yield insights into whether F-Lys utilization by bacterial pathogens (e.g., Escherichia coli, Salmonella enterica serovar Typhimurium) might offer them a competitive edge. Either during or after bacterial uptake, F-Lys is phosphorylated to form 6-phosphofructose-lysine (6-P-F-Lys). FrlB, a deglycase, converts 6-P-F-Lys to L-lysine and glucose 6-phosphate, with the latter feeding into glycolysis. Since the catalytic mechanism of FrlB has not been studied, we sought to obtain a high-resolution structure of Salmonella FrlB ± 6-P-F-Lys and identify the active-site residues essential for catalysis. After overexpression and purification of recombinant Salmonella FrlB, we obtained its 1.9 Å crystal structure. FrlB exists as a dimer with two identifiable inter-subunit active sites. In the absence of a co-crystal structure of FrlB with 6-P-F-Lys, we took two different strategies to delineate its catalytic pocket. First, we observed that the phosphosugar-binding module-called the sugar isomerase (SIS) domain in FrlB-shared sequence similarity with the eponymous domain in E. coli glucosamine 6-phosphate synthase (GlmS), which generates glucosamine 6-phosphate from fructose 6-phosphate (F-6-P) and glutamine. Overlaying the tertiary structures of Salmonella FrlB with E. coli GlmS, which had previously been co-crystallized with F-6-P, helped identify FrlB residues that could be involved in 6-P-F-Lys binding and cleavage. Second, sequence alignment of Salmonella FrlB with FraB, a related and biochemically characterized deglycase required for metabolism of fructose-asparagine (an Amadori compound) pinpointed residues that could act as a general acid and a general base during deglycation. From these comparative analyses, six candidate residues in FrlB were individually mutated to alanine or another conservative substitution, and the mutant derivatives were purified using affinity chromatography. Our differential scanning fluorimetry studies revealed that all the mutants exhibit thermal stability nearly identical to wild-type FrlB; importantly, our native mass spectrometry (nMS) studies confirmed that the mutations did not impair the ability of these mutants to form a stable dimer. A spectrophotometric coupled assay was employed to measure the activity of FrlB and the panel of mutants. When a mutation dampened or eliminated deglycase activity, nMS was leveraged to distinguish between a defect in substrate binding versus cleavage. Collectively, our results provide a platform for defining the active site and catalytic mechanism of FrlB even while highlighting the value of exploiting structures of distant homologs to advance structure-function relationship studies.