1UHV

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase.

Yang, J.K.Yoon, H.J.Ahn, H.J.Lee, B.I.Pedelacq, J.D.Liong, E.C.Berendzen, J.Laivenieks, M.Vieille, C.Zeikus, G.J.Vocadlo, D.J.Withers, S.G.Suh, S.W.

(2004) J.Mol.Biol. 335: 155-165

  • Primary Citation of Related Structures:  1PX8

  • PubMed Abstract: 
  • 1,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses. beta-D-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal ...

    1,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses. beta-D-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal structure of a member of family 39 glycoside hydrolase, i.e. beta-D-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. This study also represents the first structure of any beta-xylosidase of the above five glycoside hydrolase families. Each monomer of T. saccharolyticum beta-xylosidase comprises three distinct domains; a catalytic domain of the canonical (beta/alpha)(8)-barrel fold, a beta-sandwich domain, and a small alpha-helical domain. We have determined the structure in two forms: D-xylose-bound enzyme and a covalent 2-deoxy-2-fluoro-alpha-D-xylosyl-enzyme intermediate complex, thus providing two snapshots in the reaction pathway. This study provides structural evidence for the proposed double displacement mechanism that involves a covalent intermediate. Furthermore, it reveals possible functional roles for His228 as the auxiliary acid/base and Glu323 as a key residue in substrate recognition.


    Organizational Affiliation

    Structural Proteomics Laboratory, Department of Chemistry, College of Natural Sciences, Seoul National University, 151-742, Seoul, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-xylosidase
A, B, C, D
500Thermoanaerobacterium saccharolyticumGene Names: xynB
EC: 3.2.1.37
Find proteins for P36906 (Thermoanaerobacterium saccharolyticum)
Go to UniProtKB:  P36906
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DFX
Query on DFX

Download SDF File 
Download CCD File 
A, B, C, D
1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
C5 H9 F O3
YIJTWYXBSRZXRS-VPENINKCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.326α = 90.00
b = 152.276β = 90.00
c = 159.684γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance