3VST

The complex structure of XylC with Tris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The substrate/product-binding modes of a novel GH120 beta-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485

Huang, C.H.Sun, Y.Ko, T.P.Chen, C.C.Zheng, Y.Chan, H.C.Pang, X.Wiegel, J.Shao, W.Guo, R.T.

(2012) Biochem.J. 448: 401-407

  • DOI: 10.1042/BJ20121359
  • Primary Citation of Related Structures:  3VSU, 3VSV

  • PubMed Abstract: 
  • Xylan-1,4-β-xylosidase (β-xylosidase) hydrolyses xylo-oligomers at their non-reducing ends into individual xylose units. Recently, XylC, a β-xylosidase from Thermoanaerobacterium saccharolyticum JW/SL-YS485, was found to be structurally different fro ...

    Xylan-1,4-β-xylosidase (β-xylosidase) hydrolyses xylo-oligomers at their non-reducing ends into individual xylose units. Recently, XylC, a β-xylosidase from Thermoanaerobacterium saccharolyticum JW/SL-YS485, was found to be structurally different from corresponding glycosyl hydrolases in the CAZy database (http://www.cazy.org/), and was subsequently classified as the first member of a novel family of glycoside hydrolases (GH120). In the present paper, we report three crystal structures of XylC in complex with Tris, xylobiose and xylose at 1.48-2.05 Å (1 Å=0.1 nm) resolution. XylC assembles into a tetramer, and each monomer comprises two distinct domains. The core domain is a right-handed parallel β-helix (residues 1-75 and 201-638) and the flanking region (residues 76-200) folds into a β-sandwich domain. The enzyme contains an open carbohydrate-binding cleft, allowing accommodation of longer xylo-oligosaccharides. On the basis of the crystal structures and in agreement with previous kinetic data, we propose that XylC cleaves the glycosidic bond by the retaining mechanism using two acidic residues Asp382 (nucleophile) and Glu405 (general acid/base). In addition to the active site, nine other xylose-binding sites were consistently observed in each of the four monomers, providing a possible reason for the high tolerance of product inhibition.


    Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylosidase
A, B, C, D
638Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485)N/A
Find proteins for A2ICH1 (Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485))
Go to UniProtKB:  A2ICH1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, C, D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.638α = 90.00
b = 202.237β = 99.19
c = 99.915γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
CNSrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release