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 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    5JBF, 5JBE, 5JBD

  • 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 lactobacilli, synthesizing α-glucan-type extracellular polysaccharides from sucrose, likely evolved from GH13 starch-acting α-amylases, via GH70 4,6-α-glucanotransferases ...

    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) J Agric Food Chem 64: 2941

    Organizational Affiliation

    Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands. Electronic address: t.pijning@rug.nl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inactive glucansucraseA, B854Limosilactobacillus reuteriMutation(s): 1 
EC: 2.4.1.5
UniProt
Find proteins for Q5SBM0 (Lactobacillus reuteri)
Explore Q5SBM0 
Go to UniProtKB:  Q5SBM0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC, F5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G50146AM
GlyCosmos:  G50146AM
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseD, E, G, H2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseI3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G96370VA
GlyCosmos:  G96370VA
GlyGen:  G96370VA
Biologically Interesting Molecules (External Reference) 3 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900030
Query on PRD_900030
C, Falpha-maltopentaoseOligosaccharide /  Substrate analog Ligand Interaction
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
D, E, G, Halpha-maltoseOligosaccharide /  Nutrient Ligand Interaction
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
Ialpha-maltotrioseOligosaccharide /  Nutrient 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 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.484α = 90
b = 58.139β = 114.36
c = 150.382γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary