Crystal structure of DgpA with glucose

Experimental Data Snapshot

  • Resolution: 2.42 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C -glycoside cleaving enzyme and an O - to C -glycoside isomerase.

He, P.Wang, S.Li, S.Liu, S.Zhou, S.Wang, J.Tao, J.Wang, D.Wang, R.Ma, W.

(2023) Acta Pharm Sin B 13: 246-255

  • DOI: https://doi.org/10.1016/j.apsb.2022.05.022
  • Primary Citation of Related Structures:  
    7XR9, 7XRE, 7XRF

  • PubMed Abstract: 

    The C -glycosidic bond that connects the sugar moiety with aglycone is difficult to be broken or made due to its inert nature. The knowledge of C -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 C -glycosidic bond of puerarin (daidzein-8- C -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 C -glycoside cleaving enzyme, DgpA/B/C is capable of efficiently converting O - to C -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 C -glycosidic bond breakage and formation, but also may help to facilitate stereospecific C -glycoside synthesis in pharmaceutical industry.

  • Organizational Affiliation

    School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
367human intestinal bacterium PUEMutation(s): 0 
Gene Names: dgpA
Find proteins for A0A3Q9WWX8 (human intestinal bacterium PUE)
Explore A0A3Q9WWX8 
Go to UniProtKB:  A0A3Q9WWX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q9WWX8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
H [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
H [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
C21 H27 N7 O14 P2
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
L [auth D],
N [auth E],
P [auth F]
C6 H12 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.33α = 90
b = 128.99β = 90
c = 204.82γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2023-04-05 
  • Deposition Author(s): Ma, W., He, P.

Funding OrganizationLocationGrant Number
Other governmentChina90011451310011
Other governmentChina1000061223476

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection