Crystal structure of lamA_E269S from Zobellia galactanivorans in complex with a trisaccharide of 1,3-1,4-beta-D-glucan.

Experimental Data Snapshot

  • Resolution: 1.13 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

Starting Model: experimental
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The Beta-Glucanase Zglama from Zobellia Galactanivorans Evolved a Bent Active Site Adapted for Efficient Degradation of Algal Laminarin.

Labourel, A.Jam, M.Jeudy, A.Hehemann, J.H.Czjzek, M.Michel, G.

(2014) J Biol Chem 289: 2027

  • DOI: https://doi.org/10.1074/jbc.M113.538843
  • Primary Citation of Related Structures:  
    4BOW, 4BPZ, 4BQ1

  • PubMed Abstract: 

    Laminarinase is commonly used to describe β-1,3-glucanases widespread throughout Archaea, bacteria, and several eukaryotic lineages. Some β-1,3-glucanases have already been structurally and biochemically characterized, but very few from organisms that are in contact with genuine laminarin, the storage polysaccharide of brown algae. Here we report the heterologous expression and subsequent biochemical and structural characterization of ZgLamAGH16 from Zobellia galactanivorans, the first GH16 laminarinase from a marine bacterium associated with seaweeds. ZgLamAGH16 contains a unique additional loop, compared with other GH16 laminarinases, which is composed of 17 amino acids and gives a bent shape to the active site cleft of the enzyme. This particular topology is perfectly adapted to the U-shaped conformation of laminarin chains in solution and thus explains the predominant specificity of ZgLamAGH16 for this substrate. The three-dimensional structure of the enzyme and two enzyme-substrate complexes, one with laminaritetraose and the other with a trisaccharide of 1,3-1,4-β-d-glucan, have been determined at 1.5, 1.35, and 1.13 Å resolution, respectively. The structural comparison of substrate recognition pattern between these complexes allows the proposition that ZgLamAGH16 likely diverged from an ancestral broad specificity GH16 β-glucanase and evolved toward a bent active site topology adapted to efficient degradation of algal laminarin.

  • Organizational Affiliation

    From Sorbonne Universités, UPMC Université Paris 06, UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
256Zobellia galactanivoransMutation(s): 1 
Find proteins for G0L5X4 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore G0L5X4 
Go to UniProtKB:  G0L5X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0L5X4
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G89925KE
GlyCosmos:  G89925KE
GlyGen:  G89925KE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.13 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.528α = 90
b = 76.485β = 90
c = 142.674γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Data collection
  • Version 1.4: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.5: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary