Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 117778.62 
• Atom Count: 8328 
• Residue Count: 1000 
• Unique protein chains: 1

1PX8

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

• DOI: 10.2210/pdb1PX8/pdb

• Classification: HYDROLASE
• Organism(s): Thermoanaerobacterium saccharolyticum
• Expression System: Escherichia coli


• Deposited: 2003-07-03 Released: 2003-12-23 
• Deposition Author(s): Yang, J.K., Yoon, H.J., Ahn, H.J., Il Lee, B., Pedelacq, J.D., Liong, E.C., Berendzen, J., Laivenieks, M., Vieille, C., Zeikus, G.J., Vocadlo, D.J., Withers, S.G., Suh, S.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.271 
• R-Value Work: 0.224 

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

• PubMed: 14659747 
• Primary Citation of Related Structures:  
  1UHV


• 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 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
Molecule	Chains	Sequence Length	Organism	Details
Beta-xylosidase	A, B	500	Thermoanaerobacterium saccharolyticum	Mutation(s): 0  Gene Names: xynB EC: 3.2.1.37
Find proteins for P36906 (Thermoanaerobacterium saccharolyticum) Go to UniProtKB:  P36906

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
XYP	A, B	BETA-D-XYLOPYRANOSE C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.271 
• R-Value Work: 0.224 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 92.719	α = 90.00
b = 92.719	β = 90.00
c = 241.296	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SOLVE	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-03 
• Released Date: 2003-12-23 
• Deposition Author(s): Yang, J.K., Yoon, H.J., Ahn, H.J., Il Lee, B., Pedelacq, J.D., Liong, E.C., Berendzen, J., Laivenieks, M., Vieille, C., Zeikus, G.J., Vocadlo, D.J., Withers, S.G., Suh, S.W.

Revision History 

• Version 1.0: 2003-12-23
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance