2W5N

Native structure of the GH93 alpha-L-arabinofuranosidase of Fusarium graminearum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Molecular Basis of Arabinobio-Hydrolase Activity in Phytopathogenic Fungi. Crystal Structure and Catalytic Mechanism of Fusarium Graminearum Gh93 Exo-Alpha-L-Arabinanase.

Carapito, R.Imberty, A.Jeltsch, J.M.Byrns, S.C.Tam, P.H.Lowary, T.L.Varrot, A.Phalip, V.

(2009) J Biol Chem 284: 12285

  • DOI: https://doi.org/10.1074/jbc.M900439200
  • Primary Citation of Related Structures:  
    2W5N, 2W5O

  • PubMed Abstract: 

    The phytopathogenic fungus Fusarium graminearum secretes a very diverse pool of glycoside hydrolases (GHs) aimed at degrading plant cell walls. alpha-l-Arabinanases are essential GHs participating in the complete hydrolysis of hemicellulose, a natural resource for various industrial processes, such as bioethanol or pharmaceuticals production. Arb93A, the exo-1,5-alpha-l-arabinanase of F. graminearum encoded by the gene fg03054.1, belongs to the GH93 family, for which no structural data exists. The enzyme is highly active (1065 units/mg) and displays a strict substrate specificity for linear alpha-1,5-l-arabinan. Biochemical assays and NMR experiments demonstrated that the enzyme releases alpha-1,5-l-arabinobiose from the nonreducing end of the polysaccharide. We determined the crystal structure of the native enzyme and its complex with alpha-1,5-l-arabinobiose, a degradation product of alpha-Me-1,5-l-arabinotetraose, at 1.85 and 2.05A resolution, respectively. Arb93A is a monomeric enzyme, which presents the six-bladed beta-propeller fold characteristic of sialidases of clan GHE. The configuration of the bound arabinobiose is consistent with the retaining mechanism proposed for the GH93 family. Catalytic residues were proposed from the structural analysis, and site-directed mutagenesis was used to validate their role. They are significantly different from those observed for GHE sialidases.


  • Organizational Affiliation

    UMR 7175, Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg-CNRS, Boulevard Sébastien Brandt, BP 10413, 67412 Illkirch-Graffenstaden, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-L-ARABINOFURANOSIDASE367Fusarium graminearumMutation(s): 0 
EC: 3.2.1.55
UniProt
Find proteins for I1RH17 (Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1))
Explore I1RH17 
Go to UniProtKB:  I1RH17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI1RH17
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.34α = 90
b = 90.49β = 90
c = 92.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description