Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 237.22 kDa 
• Atom Count: 16898 
• Modelled Residue Count: 2064 
• Deposited Residue Count: 2085 
• Unique protein chains: 1

4UNI

beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 in complex with galactose

• PDB DOI: 10.2210/pdb4UNI/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium animalis subsp. lactis Bl-04
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-28 Released: 2014-10-15 
• Deposition Author(s): Viborg, A.H., Fredslund, F., Katayama, T., Nielsen, S.K., Svensson, B., Kitaoka, M., Lo Leggio, L., Abou Hachem, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium.

Viborg, A.H., Fredslund, F., Katayama, T., Nielsen, S.K., Svensson, B., Kitaoka, M., Lo Leggio, L., Abou Hachem, M.

(2014) Mol Microbiol 

• PubMed: 25287704 
• DOI: 10.1111/mmi.12815
• Primary Citation of Related Structures:  
  4UNI, 4UOQ, 4UOZ


• PubMed Abstract: 
  

The Bifidobacterium genus harbours several health promoting members of the gut microbiota. Bifidobacteria display metabolic specialization by preferentially utilizing dietary or host-derived β-galactosides. This study investigates the biochemistry and structure of a glycoside hydrolase family 42 (GH42) β-galactosidase from the probiotic Bifidobacterium animalis subsp. lactis Bl-04 (BlGal42A). BlGal42A displays a preference for undecorated β1-6 and β1-3 linked galactosides and populates a phylogenetic cluster with close bifidobacterial homologues implicated in the utilization of N-acetyl substituted β1-3 galactosides from human milk and mucin. A long loop containing an invariant tryptophan in GH42, proposed to bind substrate at subsite + 1, is identified here as specificity signature within this clade of bifidobacterial enzymes. Galactose binding at the subsite - 1 of the active site induced conformational changes resulting in an extra polar interaction and the ordering of a flexible loop that narrows the active site. The amino acid sequence of this loop provides an additional specificity signature within this GH42 clade. The phylogenetic relatedness of enzymes targeting β1-6 and β1-3 galactosides likely reflects structural differences between these substrates and β1-4 galactosides, containing an axial galactosidic bond. These data advance our molecular understanding of the evolution of sub-specificities that support metabolic specialization in the gut niche.

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Organizational Affiliation: 

Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GALACTOSIDASE	A, B, C	695	Bifidobacterium animalis subsp. lactis Bl-04	Mutation(s): 0  EC: 3.2.1.23

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	D [auth A], K [auth B], N [auth C]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
PGE	E [auth A], F [auth A], G [auth A], L [auth B], Q [auth C], T [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	H [auth A], I [auth A], M [auth B], P [auth C], R [auth C], S [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	O [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.52	α = 90
b = 199.44	β = 90
c = 217.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-28 
• Released Date: 2014-10-15 
Deposition Author(s): Viborg, A.H., Fredslund, F., Katayama, T., Nielsen, S.K., Svensson, B., Kitaoka, M., Lo Leggio, L., Abou Hachem, M.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 2.0: 2018-01-17
  Changes: Atomic model, Data collection
• Version 3.0: 2019-02-27
  Changes: Atomic model, Data collection, Database references
• Version 3.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary