1H4H

Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Catalysis and Specificity in Enzymatic Glycoside Hydrolysis: A 2,5B Conformation for the Glycosyl-Enzyme Intermediate Revealed by the Structure of the Bacillus Agaradhaerens Family 11 Xylanase.

Sabini, E.Sulzenbacher, G.Dauter, M.Dauter, Z.Jorgensen, P.L.Schulein, M.Dupont, C.Davies, G.J.Wilson, K.S.

(1999) Chem.Biol. 6: 483

  • Primary Citation of Related Structures:  1H4G, 1QH6, 1QH7

  • PubMed Abstract: 
  • The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substitut ...

    The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, Y010 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XYLANASE
A, B, C, D
209Bacillus agaradhaerensEC: 3.2.1.8
Find proteins for Q7SIE2 (Bacillus agaradhaerens)
Go to UniProtKB:  Q7SIE2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYS
Query on XYS

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

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B, C, D
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.344α = 90.00
b = 78.895β = 91.93
c = 76.273γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance