Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 92.40 kDa 
• Atom Count: 6762 
• Modelled Residue Count: 803 
• Deposited Residue Count: 815 
• Unique protein chains: 1

7CWD

Crystal structure of beta-galactosidase II from Bacillus circulans in complex with beta-D-galactopyranosyl disaccharide

• PDB DOI: 10.2210/pdb7CWD/pdb

• Classification: HYDROLASE
• Organism(s): Niallia circulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-27 Released: 2020-12-09 
• Deposition Author(s): Hong, H., Seo, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.189 

Literature

High Galacto-Oligosaccharide Production and a Structural Model for Transgalactosylation of beta-Galactosidase II from Bacillus circulans .

Choi, J.Y., Hong, H., Seo, H., Pan, J.G., Kim, E.J., Maeng, P.J., Yang, T.H., Kim, K.J.

(2020) J Agric Food Chem 68: 13806-13814

• PubMed: 33169609 
• DOI: 10.1021/acs.jafc.0c05871
• Primary Citation of Related Structures:  
  7CWD, 7CWI


• PubMed Abstract: 
  

The transgalactosylase activity of β-galactosidase produces galacto-oligosaccharides (GOSs) with prebiotic effects similar to those of major oligosaccharides in human milk. β-Galactosidases from Bacillus circulans ATCC 31382 are important enzymes in industrial-scale GOS production. Here, we show the high GOS yield of β-galactosidase II from B. circulans (β-Gal-II, Lactazyme-B), compared to other commercial enzymes. We also determine the crystal structure of the five conserved domains of β-Gal-II in an apo-form and complexed with galactose and an acceptor sugar, showing the heterogeneous mode of transgalactosylation by the enzyme. Truncation studies of the five conserved domains reveal that all five domains are essential for enzyme catalysis, while some truncated constructs were still expressed as soluble proteins. Structural comparison of β-Gal-II with other β-galactosidase homologues suggests that the GOS linkage preference of the enzyme might be quite different from other enzymes. The structural information on β-Gal-II might provide molecular insights into the transgalactosylation process of the β-galactosidases in GOS production.

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Organizational Affiliation: 

KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-glalactosidase	A	815	Niallia circulans	Mutation(s): 0  EC: 3.2.1.23
UniProt
Find proteins for A0A6M5K904 (Niallia circulans) Explore A0A6M5K904  Go to UniProtKB:  A0A6M5K904

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL (Subject of Investigation/LOI)	C [auth A], D [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
GLC (Subject of Investigation/LOI)	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.189 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.499	α = 90
b = 159.499	β = 90
c = 96.326	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOLREP	phasing
Coot	model building
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-08-27 
• Released Date: 2020-12-09 
Deposition Author(s): Hong, H., Seo, H.

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release