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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/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.


  • Organizational Affiliation

    R&D Center, GenoFocus Inc., 65 Techno 1-ro, Yusung-gu, Daejeon 34014, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-glalactosidase815Niallia 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
Sequence Annotations
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  • Reference Sequence
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description