Structure of the Family-3 Glycosyl Hydrolase BcpE2 from Streptomyces scabies

Experimental Data Snapshot

  • Resolution: 3.09 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure and Function of BcpE2, the Most Promiscuous GH3-Family Glucose Scavenging Beta-Glucosidase.

Deflandre, B.Jadot, C.Planckaert, S.Thiebaut, N.Stulanovic, N.Herman, R.Devreese, B.Kerff, F.Rigali, S.

(2022) mBio 13: e0093522-e0093522

  • DOI: https://doi.org/10.1128/mbio.00935-22
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cellulose being the most abundant polysaccharide on earth, beta-glucosidases hydrolyzing cello-oligosaccharides are key enzymes to fuel glycolysis in microorganisms developing on plant material. In Streptomyces scabiei, the causative agent of common scab in root and tuber crops, a genetic compensation phenomenon safeguards the loss of the gene encoding the cello-oligosaccharide hydrolase BglC by awakening the expression of alternative beta-glucosidases. Here, we revealed that the BglC compensating enzyme BcpE2 was the GH3-family beta-glucosidase that displayed the highest reported substrate promiscuity and was able to release the glucose moiety of all tested types of plant-derived heterosides (aryl β-glucosides, monolignol glucosides, cyanogenic glucosides, anthocyanosides, and coumarin heterosides). BcpE2 structure analysis highlighted a large cavity in the PA14 domain that covered the active site, and the high flexibility of this domain would allow proper adjustment of this cavity for disparate heterosides. The exceptional substrate promiscuity of BcpE2 provides microorganisms a versatile tool for scavenging glucose from plant-derived nutrients that widely vary in size and structure. Importantly, scopolin was the only substrate commonly hydrolyzed by both BglC and BcpE2, thereby generating the potent virulence inhibitor scopoletin. Next to fueling glycolysis, both enzymes would also fine-tune the strength of virulence. IMPORTANCE Plant decaying biomass is the most abundant provider of carbon sources for soil-dwelling microorganisms. To optimally evolve in such environmental niches, microorganisms possess an arsenal of hydrolytic enzymatic complexes to feed on the various types of polysaccharides, oligosaccharides, and monosaccharides. In this work, structural, enzymatic, and expression studies revealed the existence of a "swiss-army knife" enzyme, BcpE2, that was able to retrieve the glucose moiety of a multitude of plant-derived substrates that vary in size, structure, and origin. This enzyme would provide the microorganisms with a tool that would allow them to find nutrients from any type of plant-derived material.

  • Organizational Affiliation

    InBioS - Center for Protein Engineering, Institut de Chimie B6a, University of Liègegrid.4861.b, Liège, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidase834Streptomyces scabiei 87.22Mutation(s): 0 
Gene Names: SCAB_64101
Find proteins for C9ZDY4 (Streptomyces scabiei (strain 87.22))
Explore C9ZDY4 
Go to UniProtKB:  C9ZDY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9ZDY4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 3.09 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.62α = 90
b = 109.62β = 90
c = 164.18γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2022-09-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description