5XB7

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

• PDB DOI:  https://doi.org/10.2210/pdb5XB7/pdb

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


• Deposited: 2017-03-16 Released: 2017-11-01 
• Deposition Author(s): Viborg, A.H., Katayama, T., Arakawa, T., Abou Hachem, M., Lo Leggio, L., Kitaoka, M., Svensson, B., Fushinobu, S.
• Funding Organization(s): Japan Society of the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.191 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

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

• PubMed: 29061847 
• DOI: https://doi.org/10.1074/jbc.M117.792598
• Primary Citation of Related Structures:  
  5XB7


• 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-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 ( Bl Arap42B) from a probiotic Bifidobacterium species cannot hydrolyze β-galactosides. However, Bl Arap42B 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 Trp ³⁴⁵ - X ₁₂ -Trp ³⁵⁸ sequence motif at the Bl Arap42B active site, as compared with a Phe- X ₁₂ -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 Ara p lacking this carbon. Automated docking of paeonolide revealed that it can fit into the Bl Ara p 42B active site. The Glc p moiety of paeonolide stacks onto the aromatic ring of the Trp ²⁵² at subsite +1 and C4-OH is hydrogen bonded with Asp ²⁴⁹ Moreover, the aglycone stacks against Phe ⁴²¹ from the neighboring monomer in the Bl Ara p 42B 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.

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Organizational Affiliation: 

From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan, [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 484.24 kDa 
• Atom Count: 35,416 
• Modelled Residue Count: 4,119 
• Deposited Residue Count: 4,272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D, E, F	712	Bifidobacterium animalis subsp. lactis	Mutation(s): 0  Gene Names: AL0646_0018 EC: 3.2.1.23
UniProt
Find proteins for A0A2H4A2Z3 (Bifidobacterium animalis subsp. lactis) Explore A0A2H4A2Z3  Go to UniProtKB:  A0A2H4A2Z3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AB [auth E], BB [auth E], FA [auth B], G [auth A], GA [auth C], HA [auth C], KB [auth E], LB [auth F], MB [auth F], P [auth A], Q [auth B], R [auth B], RA [auth D], S [auth B], SA [auth D], YB [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth B], BA [auth B], CA [auth B], CB [auth E], DA [auth B], DB [auth E], EA [auth B], EB [auth E], FB [auth E], GB [auth E], H [auth A], HB [auth E], I [auth A], IA [auth C], IB [auth E], J [auth A], JA [auth C], JB [auth E], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], NB [auth F], O [auth A], OA [auth C], OB [auth F], PA [auth C], PB [auth F], QA [auth C], QB [auth F], RB [auth F], SB [auth F], T [auth B], TA [auth D], TB [auth F], U [auth B], UA [auth D], UB [auth F], V [auth B], VA [auth D], VB [auth F], W [auth B], WA [auth D], WB [auth F], X [auth B], XA [auth D], XB [auth F], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.191 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.954	α = 90
b = 177.954	β = 90
c = 375.697	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Viborg, A.H., Katayama, T., Arakawa, T., Abou Hachem, M., Lo Leggio, L., Kitaoka, M., Svensson, B., Fushinobu, S.

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Funding Organization	Location	Grant Number
Japan Society of the Promotion of Science	Japan	P15091

Revision History  

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