1URX

Crystallographic structure of beta-agarase A in complex with oligoagarose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Parallel Substrate Binding Sites in a Beta-Agarase Suggest a Novel Mode of Action on Double-Helical Agarose

Allouch, J.Helbert, W.Henrissat, B.Czjzek, M.

(2004) Structure 12: 623

  • DOI: 10.1016/j.str.2004.02.020
  • Primary Citation of Related Structures:  
    1URX

  • PubMed Abstract: 
  • Agarose is a gel-forming polysaccharide with an alpha-L(1,4)-3,6-anhydro-galactose, beta-D(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase A, from the Gram-negative bacterium Zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism ...

    Agarose is a gel-forming polysaccharide with an alpha-L(1,4)-3,6-anhydro-galactose, beta-D(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase A, from the Gram-negative bacterium Zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism. The structure of the inactive mutant beta-agarase A-E147S in complex with agaro-octaose has been solved at 1.7 A resolution. Two oligosaccharide chains are bound to the protein. The first one resides in the active site channel, spanning subsites -4 to -1. A second oligosaccharide binding site, on the opposite side of the protein, was filled with eight sugar units, parallel to the active site. The crystal structure of the beta-agarase A with agaro-octaose provides detailed information on agarose recognition in the catalytic site. The presence of the second, parallel, binding site suggests that the enzyme might be able to unwind the double-helical structure of agarose prior to the catalytic cleavage.


    Organizational Affiliation

    Architecture et Fonction de la Macromolécules Biologiques, UMR 6098, Centre National de la Recherche Scientifique and Universités Aix-Marseille I and II, 31 chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France [corrected]



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-AGARASE AA282Zobellia galactanivoransMutation(s): 1 
Gene Names: agaAzobellia_4203
EC: 3.2.1.81
UniProt
Find proteins for G0L322 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore G0L322 
Go to UniProtKB:  G0L322
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-alpha-D-galactopyranoseB4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G61438FI
GlyCosmos:  G61438FI
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranoseC7N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G77527TB
GlyCosmos:  G77527TB
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.38α = 90
b = 51.38β = 90
c = 205.36γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-16
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary