5JBE | pdb_00005jbe

4,6-alpha-glucanotransferase GTFB from Lactobacillus reuteri 121 complexed with an isomalto-maltopentasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.238 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1016/j.str.2016.11.023
  • Primary Citation Related Structures: 
    5JBD, 5JBE, 5JBF

  • 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 192.8 kDa 
  • Atom Count: 14,172 
  • Modeled Residue Count: 1,708 
  • Deposited Residue Count: 1,708 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inactive glucansucrase
A, B
854Limosilactobacillus reuteriMutation(s): 0 
EC: 2.4.1.5
UniProt
Find proteins for Q5SBM0 (Limosilactobacillus reuteri)
Explore Q5SBM0 
Go to UniProtKB:  Q5SBM0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SBM0
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C, D
5N/A
Glycosylation Resources
GlyTouCan: G15963LE
GlyCosmos: G15963LE
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC

Query on BGC



Download:Ideal Coordinates CCD File
L [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
O [auth B]
P [auth B]
Q [auth B]
J [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.238 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.441α = 90
b = 58.324β = 114.25
c = 151.41γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary