5XB7

GH42 alpha-L-arabinopyranosidase from Bifidobacterium animalis subsp. lactis Bl-04


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of alpha-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42.

Viborg, A.H.Katayama, T.Arakawa, T.Abou Hachem, M.Lo Leggio, L.Kitaoka, M.Svensson, B.Fushinobu, S.

(2017) J. Biol. Chem. 292: 21092-21101

  • DOI: 10.1074/jbc.M117.792598

  • PubMed Abstract: 
  • Enzymes of the glycoside hydrolase family 42 (GH42) are widespread in bacteria of the human gut microbiome and play fundamental roles in the decomposition of both milk and plant oligosaccharides. All GH42 enzymes characterized so far have β-galactosi ...

    Enzymes of the glycoside hydrolase family 42 (GH42) are widespread in bacteria of the human gut microbiome and play fundamental roles in the decomposition of both milk and plant oligosaccharides. All GH42 enzymes characterized so far have β-galactosidase activity. Here, we report the existence of a GH42 subfamily that is exclusively specific for α-l-arabinopyranoside and describe the first representative of this subfamily. We found that this enzyme (BlArap42B) from a probiotic Bifidobacterium species cannot hydrolyze β-galactosides. However, BlArap42B effectively hydrolyzed paeonolide and ginsenoside Rb2, plant glycosides containing an aromatic aglycone conjugated to α-l-arabinopyranosyl-(1,6)-β-d-glucopyranoside. Paeonolide, a natural glycoside from the roots of the plant genus Paeonia, is not hydrolyzed by classical GH42 β-galactosidases. X-ray crystallography revealed a unique Trp345-X12-Trp358 sequence motif at the BlArap42B active site, as compared with a Phe-X12-His motif in classical GH42 β-galactosidases. This analysis also indicated that the C6 position of galactose is blocked by the aromatic side chains, hence allowing accommodation only of Arap lacking this carbon. Automated docking of paeonolide revealed that it can fit into the BlArap42B active site. The Glcp moiety of paeonolide stacks onto the aromatic ring of the Trp252 at subsite +1 and C4-OH is hydrogen bonded with Asp249 Moreover, the aglycone stacks against Phe421 from the neighboring monomer in the BlArap42B trimer, forming a proposed subsite +2. These results further support the notion that evolution of metabolic specialization can be tracked at the structural level in key enzymes facilitating degradation of specific glycans in an ecological niche.


    Organizational Affiliation

    From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D, E, F
712N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.155 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 177.954α = 90.00
b = 177.954β = 90.00
c = 375.697γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society of the Promotion of ScienceJapanP15091

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references
  • Version 1.2: 2018-01-03
    Type: Database references