9O4U

Apo-structure of a beta-D-glucuronate dehydratase

Summary for 9O4U

• Entry DOI: 10.2210/pdb9o4u/pdb
• Descriptor: Beta-D-glucuronic acid dehydratase (2 entities in total)
• Functional Keywords: beta-d-glucuronate dehydratase, lyase
• Biological source: Bacteroides caccae
• Total number of polymer chains: 4
• Total formula weight: 182363.41

Authors

Alvarez, B.,Hettle, A.,Boraston, A.B. (deposition date: 2025-04-08, release date: 2025-06-11, Last modification date: 2025-07-09)

Primary citation

Alvarez, B.,Canil, O.F.,Low, K.E.,Hettle, A.G.,Abbott, D.W.,Boraston, A.B.
Analysis of chondroitin degradation by components of a Bacteroides caccae polysaccharide utilization locus.
J.Biol.Chem., 301:110354-110354, 2025

PubMed Abstract: The human gut microbiota (HGM) possesses enormously diverse capacity to metabolize both host and dietary glycans. Glycosaminoglycans (GAG) are complex polysaccharides that may be in the diet (e.g., from animal products) or may be presented by host tissues. These polysaccharides are known to be prioritized as a nutrient source by some members of the HGM. While significant advances in understanding how GAGs are metabolized by the HGM have been made, the varied architectures of the numerous polysaccharide utilization loci (PULs) targeting varied polysaccharides suggest that all the mechanisms of GAG degradation may not have been uncovered. Here we show that components of a (PUL) from Bacteroides caccae have activities consistent with comprising a unique pathway for depolymerization of chondroitin sulfate, a common GAG. After prior desulfation by an endo-sulfatase, BcSulf, to produce unsulfated chondroitin from chondroitin, the depolymerization pathway begins with the activity a polysaccharide lyase from family 35, BcPL35. BcPL35 activity is coupled with BcGH88, an exo-β-uronyl hydrolase, and presumably BcGH109, a confirmed α/β-N-acetylgalactosaminidase. The most unique feature of the pathway is a β-D-glucuronate dehydratase, BcGDH, which we show through structural and functional analyses primes saturated non-reducing end β-D-glucuronate residues for hydrolysis by BcGH88. BcGDH is a member of a large family previously classified as glycoside hydrolase family 154. The potential reclassification of GH154 enzymes as uronate sugar dehydratases not only improves our understanding of chondroitin metabolism by B. caccae but will be broadly applicable to predicting the function of other pathways relevant to uronate sugar metabolism.

PubMed: 40490139
DOI: 10.1016/j.jbc.2025.110354

Experimental method

X-RAY DIFFRACTION (2.19 Å)