5Z5D

Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 beta-1,4-xylosidase from Geobacillus thermoleovorans IT-08.

Rohman, A.van Oosterwijk, N.Puspaningsih, N.N.T.Dijkstra, B.W.

(2018) PLoS One 13: e0196358-e0196358

  • DOI: 10.1371/journal.pone.0196358
  • Primary Citation of Related Structures:  
    5Z5I, 5Z5H, 5Z5D, 5Z5F

  • PubMed Abstract: 
  • Complete degradation of the xylan backbone of hemicellulosic plant cell walls requires the synergistic action of endo-xylanases and β-1,4-xylosidases. While endo-xylanases produce xylooligosaccharides from xylan, β-1,4-xylosidases degrade the xylooligosaccharides into xylose monomers ...

    Complete degradation of the xylan backbone of hemicellulosic plant cell walls requires the synergistic action of endo-xylanases and β-1,4-xylosidases. While endo-xylanases produce xylooligosaccharides from xylan, β-1,4-xylosidases degrade the xylooligosaccharides into xylose monomers. The glycoside hydrolase family 43 β-1,4-xylosidase from Geobacillus thermoleovorans IT-08 is a promising, heat stable catalyst for the saccharification of hemicellulosic material into simple fermentable sugars, but it is competitively inhibited by its products arabinose and xylose. As a first step to help overcome this problem, we elucidated crystal structures of the enzyme in the unliganded form and with bound products, at 1.7-2.0 Å resolution. The structures are very similar to those of other enzymes belonging to glycoside hydrolase family 43. Unexpectedly, the monosaccharides are bound in very different ways. Arabinose preferentially binds in subsite -1, while xylose exclusively interacts with subsite +1. These structures and sugar binding preferences suggest ways for improving the catalytic performance of the enzyme by rational mutational design.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray analysis of a thermostable glycoside hydrolase family 43 beta-xylosidase from Geobacillus thermoleovorans IT-08.
      Rohman, A., van Oosterwijk, N., Kralj, S., Dijkhuizen, L., Dijkstra, B.W., Puspaningsih, N.N.
      (2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 932

    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-xylosidase A543Geobacillus thermoleovoransMutation(s): 0 
Gene Names: xyl
EC: 3.2.1.37
Find proteins for Q2I2N4 (Geobacillus thermoleovorans)
Explore Q2I2N4 
Go to UniProtKB:  Q2I2N4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.076α = 90
b = 62.076β = 90
c = 275.789γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
COMBATdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references