Nucleophile-disabled Lam16A mutant holds laminariheptaose (L7) in a cyclical conformation

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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This is version 3.1 of the entry. See complete history


Synthesis of Cyclic Beta-Glucan Using Laminarinase 16A Glycosynthase Mutant from the Basidiomycete Phanerochaete Chrysosporium.

Vasur, J.Kawai, R.Jonsson, K.H.Widmalm, G.Engstrom, A.Frank, M.Andersson, E.Hansson, H.Forsberg, Z.Igarashi, K.Samejima, M.Sandgren, M.Stahlberg, J.

(2010) J Am Chem Soc 132: 1724

  • DOI: https://doi.org/10.1021/ja909129b
  • Primary Citation of Related Structures:  
    2WLQ, 2WNE

  • PubMed Abstract: 

    Glycosynthases are precise molecular instruments for making specifically linked oligosaccharides. X-ray crystallography screening of ligands bound to the 1,3(4)-beta-D-glucanase nucleophile mutant E115S of Phanerochaete chrysosporium Laminarinase 16A (Lam16A) showed that laminariheptaose (L7) bound in an arch with the reducing and nonreducing ends occupying either side of the catalytic cleft of the enzyme. The X-ray structure of Lam16A E115S in complex with alpha-laminariheptaosyl fluoride (alphaL7F) revealed how alphaL7F could make a nucleophilic attack upon itself. Indeed, when Lam16A E115S was allowed to react with alphaL7F the major product was a cyclic beta-1,3-heptaglucan, as shown by mass spectrometry. NMR confirmed uniquely beta-1,3-linkages and no reducing end. Molecular dynamics simulations indicate that the cyclic laminariheptaose molecule is not completely planar and that torsion angles at the glycosidic linkages fluctuate between two energy minima. This is the first report of a glycosynthase that joins the reducing and nonreducing ends of a single oligosaccharide and the first reported synthesis of cyclic beta-glucan.

  • Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, POB 590, SE-754 21 Uppsala, Sweden. jonas.vasur@gmail.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE LAMINARINASE298Phanerodontia chrysosporiumMutation(s): 1 
Find proteins for Q874E3 (Phanerodontia chrysosporium)
Explore Q874E3 
Go to UniProtKB:  Q874E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ874E3
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G94559IJ
GlyCosmos:  G94559IJ
GlyGen:  G94559IJ
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G95902TY
GlyCosmos:  G95902TY
GlyGen:  G95902TY
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.273α = 90
b = 47.91β = 90
c = 152.4γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-09-21
    Changes: Database references, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2017-11-08
    Changes: Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 3.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary