2BNJ

The xylanase TA from Thermoascus aurantiacus utilizes arabinose decorations of xylan as significant substrate specificity determinants.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

wwPDB Validation 3D Report Full Report



Literature

A Family 10 Thermoascus Aurantiacus Xylanase Utilizes Arabinose Decorations of Xylan as Significant Substrate Specificity Determinants.

Vardakou, M.Flint, J.Christakopoulos, P.Lewis, R.J.Gilbert, H.J.Murray, J.W.

(2005) J Mol Biol 352: 1060

  • DOI: 10.1016/j.jmb.2005.07.051
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Xylan, which is a key component of the plant cell wall, consists of a backbone of beta-1,4-linked xylose residues that are decorated with arabinofuranose, acetyl, 4-O-methyl d-glucuronic acid and ferulate. The backbone of xylan is hydrolysed by endo- ...

    Xylan, which is a key component of the plant cell wall, consists of a backbone of beta-1,4-linked xylose residues that are decorated with arabinofuranose, acetyl, 4-O-methyl d-glucuronic acid and ferulate. The backbone of xylan is hydrolysed by endo-beta1,4-xylanases (xylanases); however, it is unclear whether the various side-chains of the polysaccharide are utilized by these enzymes as significant substrate specificity determinants. To address this question we have determined the crystal structure of a family 10 xylanase from Thermoascus aurantiacus, in complex with xylobiose containing an arabinofuranosyl-ferulate side-chain. We show that the distal glycone subsite of the enzyme makes extensive direct and indirect interactions with the arabinose side-chain, while the ferulate moiety is solvent-exposed. Consistent with the 3D structural data, the xylanase displays fourfold more activity against xylotriose in which the non-reducing moiety is linked to an arabinose side-chain, compared to the undecorated form of the oligosacchairde. These data indicate that the sugar decorations of xylans in the T.aurantiacus family 10 xylanase, rather than simply being accommodated, can be significant substrate specificity determinants.


    Organizational Affiliation

    Biotechnology Laboratory, Chemical Engineering Department, National Technical University of Athens, 5 Iroon Polytechniou Str, Zografou Campus, 15780, Athens, Greece.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE
A
303THERMOASCUS AURANTIACUSMutation(s): 0 
Gene Names: XYNA
EC: 3.2.1.8
Find proteins for P23360 (Thermoascus aurantiacus)
Go to UniProtKB:  P23360
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FER
Query on FER

Download CCD File 
A
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
C10 H10 O4
KSEBMYQBYZTDHS-HWKANZROSA-N
 Ligand Interaction
XYP
Query on XYP

Download CCD File 
A
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
AHR
Query on AHR

Download CCD File 
A
ALPHA-L-ARABINOFURANOSE
C5 H10 O5
HMFHBZSHGGEWLO-QMKXCQHVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.224α = 90
b = 49.462β = 125.38
c = 77.384γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-03-11
    Changes: Data collection, Derived calculations, Other, Polymer sequence