5Z5H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


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:  

  • 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 xylooli ...

    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

    Department of Chemistry, Faculty of Sciences and Technology, Universitas Airlangga, Surabaya, Indonesia.,Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-xylosidase
A
543Geobacillus thermoleovoransMutation(s): 0 
Gene Names: xyl
EC: 3.2.1.37
Find proteins for Q2I2N4 (Geobacillus thermoleovorans)
Go to UniProtKB:  Q2I2N4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
XYS
Query on XYS

Download SDF File 
Download CCD File 
A
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.453α = 90.00
b = 62.453β = 90.00
c = 276.672γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
COMBATdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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