4TVC

N-terminally truncated dextransucrase DSR-E from Leuconostoc mesenteroides NRRL B-1299 in complex with gluco-oligosaccharides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural Insights into the Carbohydrate Binding Ability of an alpha-(12) Branching Sucrase from Glycoside Hydrolase Family 70.

Brison, Y.Malbert, Y.Czaplicki, G.Mourey, L.Remaud-Simeon, M.Tranier, S.

(2016) J Biol Chem 291: 7527-7540

  • DOI: https://doi.org/10.1074/jbc.M115.688796
  • Primary Citation of Related Structures:  
    4TVC

  • PubMed Abstract: 

    The α-(1→2) branching sucrase ΔN123-GBD-CD2 is a transglucosylase belonging to glycoside hydrolase family 70 (GH70) that catalyzes the transfer ofd-glucosyl units from sucroseto dextrans or gluco-oligosaccharides via the formation of α-(1→2) glucosidic linkages. The first structures of ΔN123-GBD-CD2 in complex withd-glucose, isomaltosyl, or isomaltotriosyl residues were solved. The glucose complex revealed three glucose-binding sites in the catalytic gorge and six additional binding sites at the surface of domains B, IV, and V. Soaking with isomaltotriose or gluco-oligosaccharides led to structures in which isomaltosyl or isomaltotriosyl residues were found in glucan binding pockets located in domain V. One aromatic residue is systematically identified at the bottom of these pockets in stacking interaction with one glucosyl moiety. The carbohydrate is also maintained by a network of hydrogen bonds and van der Waals interactions. The sequence of these binding pockets is conserved and repeatedly present in domain V of several GH70 glucansucrases known to bind α-glucans. These findings provide the first structural evidence of the molecular interaction occurring between isomalto-oligosaccharides and domain V of the GH70 enzymes.


  • Organizational Affiliation

    the INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dextransucrase1,108Leuconostoc mesenteroidesMutation(s): 0 
Gene Names: dsrE
EC: 2.4.1.5
UniProt
Find proteins for Q8G9Q2 (Leuconostoc mesenteroides)
Explore Q8G9Q2 
Go to UniProtKB:  Q8G9Q2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G9Q2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan:  G02998EX
GlyCosmos:  G02998EX
GlyGen:  G02998EX
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
IYR
Query on IYR
A
L-PEPTIDE LINKINGC9 H10 I N O3TYR
TYI
Query on TYI
A
L-PEPTIDE LINKINGC9 H9 I2 N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.31α = 90
b = 100.14β = 90
c = 186.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2016-04-13
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary