6GL0

Structure of ZgEngAGH5_4 in complex with a cellotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The laterally acquired GH5ZgEngAGH5_4from the marine bacteriumZobellia galactanivoransis dedicated to hemicellulose hydrolysis.

Dorival, J.Ruppert, S.Gunnoo, M.Orlowski, A.Chapelais-Baron, M.Dabin, J.Labourel, A.Thompson, D.Michel, G.Czjzek, M.Genicot, S.

(2018) Biochem J 475: 3609-3628

  • DOI: 10.1042/BCJ20180486
  • Primary Citation of Related Structures:  
    6GL0, 6GL2

  • PubMed Abstract: 
  • Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions ...

    Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this model bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here, we identify a polysaccharide utilization locus in the genome of Z. galactanivorans , induced by laminarin (β-1,3-glucans), and containing a putative GH5 subfamily 4 (GH5_4) enzyme, currently annotated as a endoglucanase ( Zg EngA GH5_4 ). A phylogenetic analysis indicates that Zg EngA GH5_4 was laterally acquired from an ancestral Actinobacteria We performed the biochemical and structural characterization of Zg EngA GH5_4 and demonstrated that this GH5 is, in fact, an endo-β-glucanase, most active on mixed-linked glucan (MLG). Although Zg EngA GH5_4 and GH16 lichenases both hydrolyze MLG, these two types of enzymes release different series of oligosaccharides. Structural analyses of Zg EngA GH5_4 reveal that all the amino acid residues involved in the catalytic triad and in the negative glucose-binding subsites are conserved, when compared with the closest relative, the cellulase EngD from Clostridium cellulovorans , and some other GH5s. In contrast, the positive glucose-binding subsites of Zg EngA GH5_4 are different and this could explain the preference for MLG, with respect to cellulose or laminarin. Molecular dynamics computer simulations using different hexaoses reveal that the specificity for MLG occurs through the +1 and +2 subsites of the binding pocket that display the most important differences when compared with the structures of other GH5_4 enzymes.


    Organizational Affiliation

    Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France czjzek@sb-roscoff.fr genicot@sb-roscoff.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoglucanase, family GH5A, B, C331Zobellia galactanivoransMutation(s): 1 
Gene Names: engAzobellia_208
EC: 3.2.1.4
UniProt
Find proteins for G0L8Z3 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore G0L8Z3 
Go to UniProtKB:  G0L8Z3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranoseD, E, F3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G03861VK
GlyCosmos:  G03861VK
GlyGen:  G03861VK
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A], H [auth B], I [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900014
Query on PRD_900014
D, E, Falpha-cellotrioseOligosaccharide /  Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.574α = 90
b = 84.574β = 90
c = 117.661γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFrance604530

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary