8RO4

The crystal structure of 2-hydroxy-3-keto-glucal hydratase AtHYD from A. tumefaciens

Summary for 8RO4

• Entry DOI: 10.2210/pdb8ro4/pdb
• Descriptor: 2-hydroxy-3-keto-glucal hydratase, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: hydratase, lyase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 6
• Total formula weight: 234609.92

Authors

Grininger, C.,Bitter, J.,Pfeiffer, M.,Nidetzky, B.,Pavkov-Keller, T. (deposition date: 2024-01-11, release date: 2024-08-07, Last modification date: 2024-10-30)

Primary citation

Kastner, K.,Bitter, J.,Pfeiffer, M.,Grininger, C.,Oberdorfer, G.,Pavkov-Keller, T.,Weber, H.,Nidetzky, B.
Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.
Angew.Chem.Int.Ed.Engl., 63:e202410681-e202410681, 2024

PubMed Abstract: Flexible acquisition of substrates from nutrient pools is critical for microbes to prevail in competitive environments. To acquire glucose from diverse glycoside and disaccharide substrates, many free-living and symbiotic bacteria have developed, alongside hydrolysis, a non-hydrolytic pathway comprised of four biochemical steps and conferred from a single glycoside utilization gene locus (GUL). Mechanistically, this pathway integrates within the framework of oxidation and reduction at the glucosyl/glucose C3, the eliminative cleavage of the glycosidic bond and the addition of water in two consecutive lyase-catalyzed reactions. Here, based on study of enzymes from the phytopathogen Agrobacterium tumefaciens, we reveal a conserved Mn2+ metallocenter active site in both lyases and identify the structural requirements for specific catalysis to elimination of 3-keto-glucosides and water addition to the resulting 2-hydroxy-3-keto-glycal product, yielding 3-keto-glucose. Extending our search of GUL-encoded putative lyases to the human gut commensal Bacteroides thetaiotaomicron, we discover a Ca2+ metallocenter active site in a putative glycoside hydrolase-like protein and demonstrate its catalytic function in the eliminative cleavage of 3-keto-glucosides of opposite (alpha) anomeric configuration as preferred by the A. tumefaciens enzyme (beta). Findings identify a basic set of GUL-encoded lyases for glucoside metabolism and assign physiological significance to GUL genetic diversity in bacteria.

PubMed: 39041709
DOI: 10.1002/anie.202410681

Experimental method

X-RAY DIFFRACTION (2.51 Å)