Structure of glucan-1,6-alpha-glucosidase from Lactobacillus acidophilus NCFM

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.140 

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Enzymology and Structure of the Gh13_31 Glucan 1,6-Alpha-Glucosidase that Confers Isomaltooligosaccharide Utilization in the Probiotic Lactobacillus Acidophilus Ncfm.

Moller, M.S.Fredslund, F.Majumder, A.Nakai, H.Poulsen, J.N.Lo Leggio, L.Svensson, B.Abou Hachem, M.

(2012) J Bacteriol 194: 4249

  • DOI: https://doi.org/10.1128/JB.00622-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Isomaltooligosaccharides (IMO) have been suggested as promising prebiotics that stimulate the growth of probiotic bacteria. Genomes of probiotic lactobacilli from the acidophilus group, as represented by Lactobacillus acidophilus NCFM, encode α-1,6 glucosidases of the family GH13_31 (glycoside hydrolase family 13 subfamily 31) that confer degradation of IMO. These genes reside frequently within maltooligosaccharide utilization operons, which include an ATP-binding cassette transporter and α-glucan active enzymes, e.g., maltogenic amylases and maltose phosphorylases, and they also occur separated from any carbohydrate transport or catabolism genes on the genomes of some acidophilus complex members, as in L. acidophilus NCFM. Besides the isolated locus encoding a GH13_31 enzyme, the ABC transporter and another GH13 in the maltooligosaccharide operon were induced in response to IMO or maltotetraose, as determined by reverse transcription-PCR (RT-PCR) transcriptional analysis, suggesting coregulation of α-1,6- and α-1,4-glucooligosaccharide utilization loci in L. acidophilus NCFM. The L. acidophilus NCFM GH13_31 (LaGH13_31) was produced recombinantly and shown to be a glucan 1,6-α-glucosidase active on IMO and dextran and product-inhibited by glucose. The catalytic efficiency of LaGH13_31 on dextran and the dextran/panose (trisaccharide) efficiency ratio were the highest reported for this class of enzymes, suggesting higher affinity at distal substrate binding sites. The crystal structure of LaGH13_31 was determined to a resolution of 2.05 Å and revealed additional substrate contacts at the +2 subsite in LaGH13_31 compared to the GH13_31 from Streptococcus mutans (SmGH13_31), providing a possible structural rationale to the relatively high affinity for dextran. A comprehensive phylogenetic and activity motif analysis mapped IMO utilization enzymes from gut microbiota to rationalize preferential utilization of IMO by gut residents.

  • Organizational Affiliation

    Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUCAN 1,6-ALPHA-GLUCOSIDASE549Lactobacillus acidophilus NCFMMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q5FMB7 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM))
Explore Q5FMB7 
Go to UniProtKB:  Q5FMB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FMB7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MES

Download Ideal Coordinates CCD File 
B [auth A],
F [auth A],
J [auth A]
C6 H13 N O4 S
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth A]
H [auth A]
I [auth A]
D [auth A],
E [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth A],
L [auth A],
M [auth A]
C3 H8 O3
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.83α = 90
b = 107.25β = 90
c = 103.61γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Data collection
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description