3TTY

Crystal structure of beta-galactosidase from Bacillus circulans sp. alkalophilus in complex with galactose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

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Literature

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: 10.1111/j.1742-4658.2012.08555.x
  • Primary Citation of Related Structures:  
    3TTS, 3TTY

  • 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 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D, E, F
A, B, C, D, E, F
675Niallia circulans subsp. alkalophilusMutation(s): 0 
EC: 3.2.1.23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.2α = 90
b = 228.2β = 90
c = 246.8γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary