Crystal structure of beta-galactosidase from Bacillus circulans sp. alkalophilus

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

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Structural analysis, enzymatic characterization, and catalytic mechanisms of beta-galactosidase from Bacillus circulans sp. alkalophilus.

Maksimainen, M.Paavilainen, S.Hakulinen, N.Rouvinen, J.

(2012) FEBS J 279: 1788-1798

  • DOI: https://doi.org/10.1111/j.1742-4658.2012.08555.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Crystal structures of native and α-D-galactose-bound Bacillus circulans sp. alkalophilus β-galactosidase (Bca-β-gal) were determined at 2.40 and 2.25 Å resolutions, respectively. Bca-β-gal is a member of family 42 of glycoside hydrolases, and forms a 460 kDa hexameric structure in crystal. The protein consists of three domains, of which the catalytic domain has an (α/β)(8) barrel structure with a cluster of sulfur-rich residues inside the β-barrel. The shape of the active site is clearly more open compared to the only homologous structure available in the Protein Data Bank. This is due to the number of large differences in the loops that connect the C-terminal ends of the β-strands to the N-terminal ends of the α-helices within the (α/β)(8) barrel. The complex structure shows that galactose binds to the active site as an α-anomer and induces clear conformational changes in the active site. The implications of α-D-galactose binding with respect to the catalytic mechanism are discussed. In addition, we suggest that β-galactosidases mainly utilize a reverse hydrolysis mechanism for synthesis of galacto-oligosaccharides.

  • Organizational Affiliation

    Department of Chemistry, University of Eastern Finland, Joensuu, Finland.

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
675Niallia circulans subsp. alkalophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226α = 90
b = 226β = 90
c = 246.4γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description