Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 83.10 kDa 
• Atom Count: 7196 
• Modelled Residue Count: 719 
• Deposited Residue Count: 720 
• Unique protein chains: 1

2YFO

GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, AGASK, in complex with galactose

• PDB DOI: 10.2210/pdb2YFO/pdb

• Classification: HYDROLASE
• Organism(s): [Ruminococcus] gnavus E1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-07 Released: 2011-09-28 
• Deposition Author(s): Sulzenbacher, G., Bruel, L., Tison-Cervera, M., Pujol, A., Nicoletti, C., Perrier, J., Galinier, A., Ropartz, D., Fons, M., Pompeo, F., Giardina, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.142 
• R-Value Work: 0.124 
• R-Value Observed: 0.125 

Literature

Agask, a Bifunctional Enzyme from the Human Microbiome Coupling Galactosidase and Kinase Activities

Bruel, L., Sulzenbacher, G., Tison-Cervera, M., Pujol, A., Nicoletti, C., Perrier, J., Galinier, A., Ropartz, D., Fons, M., Pompeo, F., Giardina, T.

(2011) J Biol Chem 286: 40814

• PubMed: 21931163 
• DOI: 10.1074/jbc.M111.286039
• Primary Citation of Related Structures:  
  2YFN, 2YFO


• PubMed Abstract: 
  

α-Galactosides are non-digestible carbohydrates widely distributed in plants. They are a potential source of energy in our daily food, and their assimilation by microbiota may play a role in obesity. In the intestinal tract, they are degraded by microbial glycosidases, which are often modular enzymes with catalytic domains linked to carbohydrate-binding modules. Here we introduce a bifunctional enzyme from the human intestinal bacterium Ruminococcus gnavus E1, α-galactosidase/sucrose kinase (AgaSK). Sequence analysis showed that AgaSK is composed of two domains: one closely related to α-galactosidases from glycoside hydrolase family GH36 and the other containing a nucleotide-binding motif. Its biochemical characterization showed that AgaSK is able to hydrolyze melibiose and raffinose to galactose and either glucose or sucrose, respectively, and to specifically phosphorylate sucrose on the C6 position of glucose in the presence of ATP. The production of sucrose-6-P directly from raffinose points toward a glycolytic pathway in bacteria, not described so far. The crystal structures of the galactosidase domain in the apo form and in complex with the product shed light onto the reaction and substrate recognition mechanisms and highlight an oligomeric state necessary for efficient substrate binding and suggesting a cross-talk between the galactose and kinase domains.

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Organizational Affiliation: 

Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK	A	720	[Ruminococcus] gnavus E1	Mutation(s): 0  EC: 3.2.1.22 (PDB Primary Data), 2.7 (UniProt)
UniProt
Find proteins for G4T4R7 (Ruminococcus gnavus) Explore G4T4R7  Go to UniProtKB:  G4T4R7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	JA [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
GLA	IA [auth A]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
PGE	C [auth A], D [auth A], E [auth A], F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4	G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.142 
• R-Value Work: 0.124 
• R-Value Observed: 0.125 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.016	α = 90
b = 111.603	β = 90
c = 155.29	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-07 
• Released Date: 2011-09-28 
Deposition Author(s): Sulzenbacher, G., Bruel, L., Tison-Cervera, M., Pujol, A., Nicoletti, C., Perrier, J., Galinier, A., Ropartz, D., Fons, M., Pompeo, F., Giardina, T.

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release
  
• Version 1.1: 2011-11-23
  Changes: Database references, Derived calculations, Other
• Version 1.2: 2011-12-07
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary