2BFG

crystal structure of beta-xylosidase (fam GH39) in complex with dinitrophenyl-beta-xyloside and covalently bound xyloside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzyme-Substrate Complex Structures of a Gh39 Beta-Xylosidase from Geobacillus Stearothermophilus.

Czjzek, M.David, A.B.Bravman, T.Shoham, G.Henrissat, B.Shoham, Y.

(2005) J.Mol.Biol. 353: 838

  • DOI: 10.1016/j.jmb.2005.09.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beta-D-Xylosidases are glycoside hydrolases that catalyse the release of xylose units from short xylooligosaccharides and are engaged in the final breakdown of plant cell-wall hemicelluloses. beta-D-Xylosidases are found in glycoside hydrolase famili ...

    Beta-D-Xylosidases are glycoside hydrolases that catalyse the release of xylose units from short xylooligosaccharides and are engaged in the final breakdown of plant cell-wall hemicelluloses. beta-D-Xylosidases are found in glycoside hydrolase families 3, 39, 43, 52 and 54. The first crystal structure of a GH39 beta-xylosidase revealed a multi-domain organization with the catalytic domain having the canonical (beta/alpha)8 barrel fold. Here, we report the crystal structure of the GH39 Geobacillus stearothermophilus beta-D-xylosidase, inactivated by a point mutation of the general acid-base residue E160A, in complex with the chromogenic substrate molecule 2,5-dinitrophenyl-beta-D-xyloside. Surprisingly, six of the eight active sites present in the crystallographic asymmetric unit contain the trapped covalent glycosyl-enzyme intermediate, while two of them still contain the uncleaved substrate. The structural characterization of these two critical species along the reaction coordinate of this enzyme identifies the residues forming its xyloside-binding pocket as well as those essential for its aglycone recognition.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Family 39 Beta-D-Xylosidase from Geobacillus Stearothermophilus T-6
      Czjzek, M.,Bravman, T.,Henrissat, B.,Shoham, Y.
      (2004) Acta Crystallogr.,Sect.D 60: 583


    Organizational Affiliation

    Station Biologique de Roscoff, Végétaux Marins et Biomolécules, UMR7139-CNRS-UPMC, Place George Teissier, BP74, 29682 Roscoff, France. czjzek@sb-roscoff.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-XYLOSIDASE
A, B, C, D, E, F, G, H
503Geobacillus stearothermophilusMutation(s): 0 
Gene Names: xynB
EC: 3.2.1.37
Find proteins for Q9ZFM2 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9ZFM2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANX
Query on ANX

Download SDF File 
Download CCD File 
A, D
2,5-DINITROPHENOL
C6 H4 N2 O5
UWEZBKLLMKVIPI-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
XYS
Query on XYS

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
XYP
Query on XYP

Download SDF File 
Download CCD File 
A, D
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.950α = 90.00
b = 162.160β = 90.00
c = 308.200γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-11-14
    Type: Database references, Derived calculations, Other, Refinement description