6R3R

First crystal structure of endo-levanase BT1760 from Bacteroides thetaiotaomicron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


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Literature

First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron.

Ernits, K.Eek, P.Lukk, T.Visnapuu, T.Alamae, T.

(2019) Sci Rep 9: 8443-8443

  • DOI: 10.1038/s41598-019-44785-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The endo-levanase BT1760 of a human gut commensal Bacteroides thetaiotaomicron randomly cuts a β-2,6-linked fructan, levan, into fructo-oligosaccharides providing a prebiotic substrate for gut microbiota. Here we introduce the crystal structure of BT ...

    The endo-levanase BT1760 of a human gut commensal Bacteroides thetaiotaomicron randomly cuts a β-2,6-linked fructan, levan, into fructo-oligosaccharides providing a prebiotic substrate for gut microbiota. Here we introduce the crystal structure of BT1760 at resolution of 1.65 Å. The fold of the enzyme is typical for GH32 family proteins: a catalytic N-terminal five-bladed β-propeller connected with a C-terminal β-sandwich domain. The levantetraose-bound structure of catalytically inactive mutant E221A at 1.90-Å resolution reveals differences in substrate binding between the endo-acting fructanases. A shallow substrate-binding pocket of the endo-inulinase INU2 of Aspergillus ficuum binds at least three fructose residues at its flat bottom. In the levantetraose-soaked crystal of the endo-levanase E221A mutant the ligand was bent into the pond-like substrate pocket with its fructose residues making contacts at -3, -2, -1 and + 1 subsites residing at several pocket depths. Binding of levantetraose to the β-sandwich domain was not detected. The N- and C-terminal modules of BT1760 did not bind levan if expressed separately, the catalytic domain lost its activity and both modules tended to precipitate. We gather that endo-levanase BT1760 requires both domains for correct folding, solubility and stability of the protein.


    Organizational Affiliation

    Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.,Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia. tiina@alamae.eu.,Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase family 32
A
508Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
Find proteins for Q8A6W6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A6W6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.154 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.657α = 90.00
b = 110.607β = 90.00
c = 171.244γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
AutoSolphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Estonian Research CouncilEstoniaPUT1050
Estonian Research CouncilEstoniaIUT19-9

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references