8BVK

The crystal structure of O-glycoside cleaving beta-eliminase from A. tumefaciens AtOGE

Summary for 8BVK

• Entry DOI: 10.2210/pdb8bvk/pdb
• Descriptor: Xylose isomerase, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: o-glycoside cleaving beta-eliminase, a. tumefaciens, atoge, hydrolase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 2
• Total formula weight: 55978.20

Authors

Kuhlmann, K.,Bitter, J.,Pfeiffer, M.,Nidetzky, B.,Pavkov-Keller, T. (deposition date: 2022-12-04, release date: 2023-11-01, Last modification date: 2023-11-22)

Primary citation

Bitter, J.,Pfeiffer, M.,Borg, A.J.E.,Kuhlmann, K.,Pavkov-Keller, T.,Sanchez-Murcia, P.A.,Nidetzky, B.
Enzymatic beta-elimination in natural product O- and C-glycoside deglycosylation.
Nat Commun, 14:7123-7123, 2023

PubMed Abstract: Biological degradation of natural product glycosides involves, alongside hydrolysis, β-elimination for glycosidic bond cleavage. Here, we discover an O-glycoside β-eliminase (OGE) from Agrobacterium tumefaciens that converts the C3-oxidized O-β-D-glucoside of phloretin (a plant-derived flavonoid) into the aglycone and the 2-hydroxy-3-keto-glycal elimination product. While unrelated in sequence, OGE is structurally homologous to, and shows effectively the same Mn active site as, the C-glycoside deglycosylating enzyme (CGE) from a human intestinal bacterium implicated in β-elimination of 3-keto C-β-D-glucosides. We show that CGE catalyzes β-elimination of 3-keto O- and C-β-D-glucosides while OGE is specific for the O-glycoside substrate. Substrate comparisons and mutagenesis for CGE uncover positioning of aglycone for protonic assistance by the enzyme as critically important for C-glycoside cleavage. Collectively, our study suggests convergent evolution of active site for β-elimination of 3-keto O-β-D-glucosides. C-Glycoside cleavage is a specialized feature of this active site which is elicited by substrate through finely tuned enzyme-aglycone interactions.

PubMed: 37932298
DOI: 10.1038/s41467-023-42750-0

Experimental method

X-RAY DIFFRACTION (2 Å)