1QW9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1093/emboj/cdg494
  • Primary Citation of Related Structures:  

  • 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 1 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-L-arabinofuranosidase
A, B
502Geobacillus stearothermophilusMutation(s): 1 
Gene Names: abfA
EC: 3.2.1.55
Find proteins for Q9XBQ3 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9XBQ3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KHP
Query on KHP

Download SDF File 
Download CCD File 
A, B
2-HYDROXYMETHYL-5-(4-NITRO-PHENOXY)-TETRAHYDRO-FURAN-3,4-DIOL
4-NITROPHENYL-ARA
C11 H13 N O7
DUYYBTBDYZXISX-UKKRHICBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 179.311α = 90.00
b = 179.311β = 90.00
c = 100.397γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance