7XRF

Crystal structaure of DgpB/C complex

Summary for 7XRF

• Entry DOI: 10.2210/pdb7xrf/pdb
• Descriptor: AP_endonuc_2 domain-containing protein, DgpB, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: c-glycoside cleavage, isomerization, lyase
• Biological source: human intestinal bacterium PUE; More
• Total number of polymer chains: 8
• Total formula weight: 212189.32

Authors

Ma, M.,He, P. (deposition date: 2022-05-10, release date: 2023-02-15, Last modification date: 2024-05-08)

Primary citation

He, P.,Wang, S.,Li, S.,Liu, S.,Zhou, S.,Wang, J.,Tao, J.,Wang, D.,Wang, R.,Ma, W.
Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C -glycoside cleaving enzyme and an O - to C -glycoside isomerase.
Acta Pharm Sin B, 13:246-255, 2023

PubMed Abstract: The -glycosidic bond that connects the sugar moiety with aglycone is difficult to be broken or made due to its inert nature. The knowledge of -glycoside breakdown and synthesis is very limited. Recently, the enzyme DgpA/B/C cascade from a human intestinal bacterium PUE was identified to specifically cleave the -glycosidic bond of puerarin (daidzein-8--glucoside). Here we investigated how puerarin is recognized and oxidized by DgpA based on crystal structures of DgpA with or without substrate and biochemical characterization. More strikingly, we found that apart from being a -glycoside cleaving enzyme, DgpA/B/C is capable of efficiently converting - to -glycoside showing the activity as a structure isomerase. A possible mechanistic model was proposed dependently of the simulated complex structure of DgpB/C with 3″-oxo-daidzin and structure-based mutagenesis. Our findings not only shed light on understanding the enzyme-mediated -glycosidic bond breakage and formation, but also may help to facilitate stereospecific -glycoside synthesis in pharmaceutical industry.

PubMed: 36815035
DOI: 10.1016/j.apsb.2022.05.022

Experimental method

X-RAY DIFFRACTION (2.137 Å)