5OLC

Crystal structure of the 3,6-anhydro-D-galactonate cycloisomerase from Zobellia galactanivorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria.

Ficko-Blean, E.Prechoux, A.Thomas, F.Rochat, T.Larocque, R.Zhu, Y.Stam, M.Genicot, S.Jam, M.Calteau, A.Viart, B.Ropartz, D.Perez-Pascual, D.Correc, G.Matard-Mann, M.Stubbs, K.A.Rogniaux, H.Jeudy, A.Barbeyron, T.Medigue, C.Czjzek, M.Vallenet, D.McBride, M.J.Duchaud, E.Michel, G.

(2017) Nat Commun 8: 1685-1685

  • DOI: https://doi.org/10.1038/s41467-017-01832-6
  • Primary Citation of Related Structures:  
    5OLC, 5OPQ

  • PubMed Abstract: 

    Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria using largely uncharacterized mechanisms. Here we describe the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, in the marine heterotrophic bacterium Zobellia galactanivorans. Carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and genes distal to the PUL, including a susCD-like pair. The carrageenan utilization system is well conserved in marine Bacteroidetes but modified in other phyla of marine heterotrophic bacteria. The core system is completed by additional functions that might be assumed by non-orthologous genes in different species. This complex genetic structure may be the result of multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion.


  • Organizational Affiliation

    Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galactonate dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H
396Zobellia galactanivoransMutation(s): 0 
Gene Names: dgoDzobellia_3156
EC: 4.2.1.6
UniProt
Find proteins for G0L7B8 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore G0L7B8 
Go to UniProtKB:  G0L7B8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0L7B8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.84α = 90
b = 154.07β = 104.38
c = 150.87γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE19-0020-01
French National Research AgencyFranceANR-10-BTBR-04

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description