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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D, E, F
675N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GLA
Query on GLA
Download SDF File 
Download CCD File 
A, B, C, D, E, F
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.160 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 228.200α = 90.00
b = 228.200β = 90.00
c = 246.800γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
ADSCdata collection
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references