The crystal structure of Arabinofuranosidase

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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Structural Analysis of Alpha-L-Arabinofuranosidase from Thermotoga Maritima Reveals Characteristics for Thermostability and Substrate Specificity.

Dumbrepatil, A.Park, J.Jung, T.-Y.Song, H.-N.Jang, M.Han, N.S.Kim, T.-J.Woo, E.-J.

(2012) J Microbiol Biotechnol 22: 1724

  • DOI: https://doi.org/10.4014/jmb.1208.08043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    An alpha-L-arabinofuranosidase (TmAFase) from Thermotoga maritima MSB8 is a highly thermostable exo-acting hemicellulase that exhibits a relatively higher activity towards arabinan and arabinoxylan, compared with other glycoside hydrolase 51 family enzymes. In the present study, we carried out the enzymatic characterization and structural analysis of TmAFase. Tight domain associations found in TmAFase, such as an inter-domain disulfide bond (Cys306 and Cys476) in each monomer, a novel extended arm (amino acids 374-385) at the dimer interface, and total 12 salt bridges in the hexamer, may account for the thermostability of the enzyme. One of the xylan binding determinants (Trp96) was identified in the active site, and a region of amino acids (374-385) protrudes out forming an obvious wall at the substrate-binding groove to generate a cavity. The altered cavity shape with a strong negative electrostatic distribution is likely related to the unique substrate preference of TmAFase towards branched polymeric substrates.

  • Organizational Affiliation

    Department of Food Science and Technology, Chungbuk National University, Cheongju, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
482Thermotoga maritima MSB8Mutation(s): 0 
Find proteins for Q9WYB7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYB7 
Go to UniProtKB:  Q9WYB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYB7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.71α = 90
b = 161.538β = 106.3
c = 112.602γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references