Crystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

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Crystal Structure of Beta1-6-Galactosidase from Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants of the Enzymatic Activity and its Inhibition by Alpha-Galactose.

Godoy, A.S.Camilo, C.M.Kadowaki, M.A.Muniz, H.D.Santo, M.E.Murakami, M.T.Nascimento, A.S.Polikarpov, I.

(2016) FEBS J 283: 4097

  • DOI: https://doi.org/10.1111/febs.13908
  • Primary Citation of Related Structures:  
    4UCF, 4UZS

  • PubMed Abstract: 

    In a search for better comprehension of β-galactosidase function and specificity, we solved the crystal structures of the GH42 β-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tract, and its complex with d-α-galactose. BbgII is a three-domain molecule that forms barrel-shaped trimers in solution. BbgII interactions with d-α-galactose, a competitive inhibitor, showed a number of residues that are involved in the coordination of ligands. A combination of site-directed mutagenesis of these amino acid residues with enzymatic activity measurements confirmed that Glu161 and Glu320 are fundamental for catalysis and their substitution by alanines led to catalytically inactive mutants. Mutation Asn160Ala resulted in a two orders of magnitude decrease of the enzyme k cat without significant modification in its K m , whereas mutations Tyr289Phe and His371Phe simultaneously decreased k cat and increased K m values. Enzymatic activity of Glu368Ala mutant was too low to be detected. Our docking and molecular dynamics simulations showed that the enzyme recognizes and tightly binds substrates with β1→6 and β1→3 bonds, while binding of the substrates with β1→4 linkages is less favorable. Structural data are available in the PDB under the accession numbers 4UZS and 4UCF.

  • Organizational Affiliation

    Departamento de Física em São Carlos, Universidade de São Paulo, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
689Bifidobacterium bifidum S17Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth B]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth C],
J [auth C]
C6 H12 O6
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Query on POL

Download Ideal Coordinates CCD File 
C3 H8 O
Binding Affinity Annotations 
IDSourceBinding Affinity
GLA Binding MOAD:  4UCF Ki: 5.90e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.72α = 90
b = 101.592β = 105.4
c = 114.625γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 2.0: 2017-08-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 2.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 2.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary