2XN2

Structure of alpha-galactosidase from Lactobacillus acidophilus NCFM with galactose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Crystal Structure of Alpha-Galactosidase from Lactobacillus Acidophilus Ncfm: Insight Into Tetramer Formation and Substrate Binding.

Fredslund, F., Abou Hachem, M., Jonsgaard Larsen, R., Gerd Sorensen, P., Coutinho, P.M., Lo Leggio, L., Svensson, B.

(2011) J Mol Biol 412: 466

  • DOI: https://doi.org/10.1016/j.jmb.2011.07.057
  • Primary Citation of Related Structures:  
    2XN0, 2XN1, 2XN2

  • PubMed Abstract: 

    • Lactobacillus acidophilus NCFM is a probiotic bacterium known for its beneficial effects on human health. The importance of α-galactosidases (α-Gals) for growth of probiotic organisms on oligosaccharides of the raffinose family present in many foods is increasingly recognized ...

    Lactobacillus acidophilus NCFM is a probiotic bacterium known for its beneficial effects on human health. The importance of α-galactosidases (α-Gals) for growth of probiotic organisms on oligosaccharides of the raffinose family present in many foods is increasingly recognized. Here, the crystal structure of α-Gal from L. acidophilus NCFM (LaMel36A) of glycoside hydrolase (GH) family 36 (GH36) is determined by single-wavelength anomalous dispersion. In addition, a 1.58-Å-resolution crystallographic complex with α-d-galactose at substrate binding subsite -1 was determined. LaMel36A has a large N-terminal twisted β-sandwich domain, connected by a long α-helix to the catalytic (β/α)(8)-barrel domain, and a C-terminal β-sheet domain. Four identical monomers form a tightly packed tetramer where three monomers contribute to the structural integrity of the active site in each monomer. Structural comparison of LaMel36A with the monomeric Thermotoga maritima α-Gal (TmGal36A) reveals that O2 of α-d-galactose in LaMel36A interacts with a backbone nitrogen in a glycine-rich loop of the catalytic domain, whereas the corresponding atom in TmGal36A is from a tryptophan side chain belonging to the N-terminal domain. Thus, two distinctly different structural motifs participate in substrate recognition. The tetrameric LaMel36A furthermore has a much deeper active site than the monomeric TmGal36A, which possibly modulates substrate specificity. Sequence analysis of GH36, inspired by the observed structural differences, results in four distinct subgroups having clearly different active-site sequence motifs. This novel subdivision incorporates functional and architectural features and may aid further biochemical and structural analyses within GH36.

    Organizational Affiliation: 

    Department of Systems Biology, Enzyme and Protein Chemistry, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-GALACTOSIDASE732Lactobacillus acidophilus NCFMMutation(s): 0 
Gene Names: melA, aga, LBA1438
EC: 3.2.1.22
UniProt
Find proteins for G1UB44 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM))
Explore G1UB44 
Go to UniProtKB:  G1UB44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1UB44
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLA
Query on GLA
Download Ideal Coordinates CCD File 
B [auth A]alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth A],
BA [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
IMD
Query on IMD
Download Ideal Coordinates CCD File 
C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SME
Query on SME
A
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.61α = 90
b = 126.7β = 90
c = 148.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Database references, Structure summary
  • Version 1.2: 2011-09-14
    Changes: Database references
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary