High resolution crystal structure of beta-porphyranase A from Zobellia galactanivorans

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

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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: https://doi.org/10.1074/jbc.M112.377184
  • Primary Citation of Related Structures:  
    4ASM, 4ATE, 4ATF

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-PORPHYRANASE A266Zobellia galactanivoransMutation(s): 0 
Find proteins for D7GXG0 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore D7GXG0 
Go to UniProtKB:  D7GXG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7GXG0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.27α = 90
b = 70.27β = 90
c = 92.47γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other