5JBF

4,6-alpha-glucanotransferase GTFB (D1015N mutant) from Lactobacillus reuteri 121 complexed with maltopentaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of 4,6-alpha-Glucanotransferase Supports Diet-Driven Evolution of GH70 Enzymes from alpha-Amylases in Oral Bacteria.

Bai, Y.Gangoiti, J.Dijkstra, B.W.Dijkhuizen, L.Pijning, T.

(2017) Structure 25: 231-242

  • DOI: 10.1016/j.str.2016.11.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Food processing and refining has dramatically changed the human diet, but little is known about whether this affected the evolution of enzymes in human microbiota. We present evidence that glycoside hydrolase family 70 (GH70) glucansucrases from lact ...

    Food processing and refining has dramatically changed the human diet, but little is known about whether this affected the evolution of enzymes in human microbiota. We present evidence that glycoside hydrolase family 70 (GH70) glucansucrases from lactobacilli, synthesizing α-glucan-type extracellular polysaccharides from sucrose, likely evolved from GH13 starch-acting α-amylases, via GH70 4,6-α-glucanotransferases. The crystal structure of a 4,6-α-glucanotransferase explains the mode of action and unique product specificity of these enzymes. While the α-amylase substrate-binding scaffold is retained, active-site loops adapted to favor transglycosylation over hydrolysis; the structure also gives clues as to how 4,6-α-glucanotransferases may have evolved further toward sucrose utilization instead of starch. Further supported by genomic, phylogenetic, and in vivo studies, we propose that dietary changes involving starch (and starch derivatives) and sucrose intake were critical factors during the evolution of 4,6-α-GTs and glucansucrases from α-amylases, allowing oral bacteria to produce extracellular polymers that contribute to biofilm formation from different substrates.


    Related Citations: 
    • Lactobacillus reuteri Strains Convert Starch and Maltodextrins into Homoexopolysaccharides Using an Extracellular and Cell-Associated 4,6-alpha-Glucanotransferase
      Bai, Y.,Boger, M.,van der Kaaij, R.M.,Woortman, A.J.J.,Pijning, T.,van Leeuwen, S.S.,Lammerts van Bueren, A.,Dijkhuizen, L.
      (2016) Journal of Agricultural and Food Chemistry 64: 2941


    Organizational Affiliation

    Laboratory of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inactive glucansucrase
A, B
854Lactobacillus reuteriMutation(s): 1 
EC: 2.4.1.5
Find proteins for Q5SBM0 (Lactobacillus reuteri)
Go to UniProtKB:  Q5SBM0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A, B
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
MLR
Query on MLR

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Download CCD File 
B
MALTOTRIOSE
AMYLOTRIOSE
C18 H32 O16
FYGDTMLNYKFZSV-PXXRMHSHSA-N
 Ligand Interaction
CEX
Query on CEX

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Download CCD File 
A, B
alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranose
maltopentaose
C30 H52 O26
FTNIPWXXIGNQQF-DWTFCAFKSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 219.484α = 90.00
b = 58.139β = 114.36
c = 150.382γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China Scholarship CouncilChina--
CCC ResearchNetherlands--

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-15
    Type: Database references