7CWD

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
beta-glalactosidaseA815Niallia circulansMutation(s): 0 
EC: 3.2.1.23
UniProt
Find proteins for A0A6M5K904 (Niallia circulans)
Explore A0A6M5K904 
Go to UniProtKB:  A0A6M5K904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M5K904
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL (Subject of Investigation/LOI)
Query on GAL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
B [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
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 = 159.499α = 90
b = 159.499β = 90
c = 96.326γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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