Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with 4-nitrophenyl-Ara

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.173 

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This is version 2.2 of the entry. See complete history


Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase

Hoevel, K.Shallom, D.Niefind, K.Belakhov, V.Shoham, G.Baasov, T.Shoham, Y.Schomburg, D.

(2003) EMBO J 22: 4922-4932

  • DOI: https://doi.org/10.1093/emboj/cdg494
  • Primary Citation of Related Structures:  
    1PZ2, 1PZ3, 1QW8, 1QW9

  • PubMed Abstract: 

    High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.

  • Organizational Affiliation

    Institute for Biochemistry, University of Cologne, Cologne 50674, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
502Geobacillus stearothermophilusMutation(s): 1 
Gene Names: ABFA
Find proteins for Q9XBQ3 (Geobacillus stearothermophilus)
Explore Q9XBQ3 
Go to UniProtKB:  Q9XBQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XBQ3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on KHP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-nitrophenyl alpha-L-arabinofuranoside
C11 H13 N O7
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.173 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.311α = 90
b = 179.311β = 90
c = 100.397γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary
  • Version 2.2: 2024-02-14
    Changes: Data collection