4ATF

Crystal structure of inactivated mutant beta-agarase B in complex with agaro-octaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia Galactanivorans.

Hehemann, J.H.Correc, G.Thomas, F.Bernard, T.Barbeyron, T.Jam, M.Helbert, W.Michel, G.Czjzek, M.

(2012) J.Biol.Chem. 287: 30571

  • DOI: 10.1074/jbc.M112.377184
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycosi ...

    Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. Although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here, we report the biochemical and structural comparison of five β-porphyranases and β-agarases from Z. galactanivorans. The respective degradation patterns of two β-porphyranases and three β-agarases are analyzed by their action on defined hybrid oligosaccharides. In light of the high resolution crystal structures, the biochemical results allowed a detailed mapping of substrate specificities along the active site groove of the enzymes. Although PorA displays a strict requirement for C6-sulfate in the -2- and +1-binding subsites, PorB tolerates the presence of 3-6-anhydro-l-galactose in subsite -2. Both enzymes do not accept methylation of the galactose unit in the -1 subsite. The β-agarase AgaD requires at least four consecutive agarose units (DP8) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the -4, +1, and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans.


    Related Citations: 
    • Transfer of Carbohydrate-Active Enzymes from Marine Bacteria to Japanese Gut Microbiota.
      Hehemann, J.,Correc, G.,Barbeyron, T.,Helbert, W.,Czjzek, M.,Michel, G.
      (2010) Nature 464: 908


    Organizational Affiliation

    Université Pierre et Marie Curie, Végétaux Marins et Biomolécules UMR 7139, Station Biologique de Roscoff, F 29682 Roscoff, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-AGARASE B
A, B, C, D
308Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)Mutation(s): 1 
Gene Names: agaB
EC: 3.2.1.81
Find proteins for Q9RGX8 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Go to UniProtKB:  Q9RGX8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
AAL
Query on AAL

Download SDF File 
Download CCD File 
A, B, C, D
3,6-ANHYDRO-L-GALACTOSE
C6 H10 O5
DCQFFOLNJVGHLW-DSOBHZJASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.187α = 90.00
b = 106.234β = 93.22
c = 96.983γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-09-12
    Type: Database references, Structure summary
  • Version 1.2: 2017-08-09
    Type: Data collection