6GL2

Structure of ZgEngAGH5_4 wild type at 1.2 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

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

    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.,Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoglucanase, family GH5
A
337Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)Mutation(s): 0 
Gene Names: engA
EC: 3.2.1.4
Find proteins for G0L8Z3 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Go to UniProtKB:  G0L8Z3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.490α = 90.00
b = 48.460β = 104.35
c = 59.260γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references