1E0X

XYLANASE 10A FROM SREPTOMYCES LIVIDANS. XYLOBIOSYL-ENZYME INTERMEDIATE AT 1.65 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substrate Specificity in Glycoside Hydrolase Family 10. Structural and Kinetic Analysis of the Streptomyces Lividans Xylanase 10A

Ducros, V.Charnock, S.J.Derewenda, U.Derewenda, Z.S.Dauter, Z.Dupont, C.Shareck, F.Morosoli, R.Kluepfel, D.Davies, G.J.

(2000) J.Biol.Chem. 275: 23020

  • Primary Citation of Related Structures:  1E0V, 1E0W

  • PubMed Abstract: 
  • Endoxylanases are a group of enzymes that hydrolyze the beta-1, 4-linked xylose backbone of xylans. They are predominantly found in two discrete sequence families known as glycoside hydrolase families 10 and 11. The Streptomyces lividans xylanase Xyl ...

    Endoxylanases are a group of enzymes that hydrolyze the beta-1, 4-linked xylose backbone of xylans. They are predominantly found in two discrete sequence families known as glycoside hydrolase families 10 and 11. The Streptomyces lividans xylanase Xyl10A is a family 10 enzyme, the native structure of which has previously been determined by x-ray crystallography at a 2.6 A resolution (Derewenda, U., Swenson, L., Green, R., Wei, Y., Morosoli, R., Shareck, F., Kluepfel, D., and Derewenda, Z. S. (1994) J. Biol. Chem. 269, 20811-20814). Here, we report the native structure of Xyl10A refined at a resolution of 1.2 A, which reveals many features such as the rare occurrence of a discretely disordered disulfide bond between residues Cys-168 and Cys-201. In order to investigate substrate binding and specificity in glycoside hydrolase family 10, the covalent xylobiosyl enzyme and the covalent cellobiosyl enzyme intermediates of Xyl10A were trapped through the use of appropriate 2-fluoroglycosides. The alpha-linked intermediate with the nucleophile, Glu-236, is in a (4)C(1) chair conformation as previously observed in the family 10 enzyme Cex from Cellulomonas fimi (Notenboom, V., Birsan, C., Warren, R. A. J., Withers, S. G., and Rose, D. R. (1998) Biochemistry 37, 4751-4758). The different interactions of Xyl10A with the xylobiosyl and cellobiosyl moieties, notably conformational changes in the -2 and -1 subsites, together with the observed kinetics on a range of aryl glycosides, shed new light on substrate specificity in glycoside hydrolase family 10.


    Related Citations: 
    • Crystal Structure, at 2.6 A Resolution, of the Streptomyces Lividans Xylanase A, a Member of the F Family of B-1,4-D-Glycanases
      Derewenda, U.,Swenson, L.,Green, R.,Wei, Y.,Morosoli, R.,Shareck, F.,Kluepfel, D.,Derewenda, Z.S.
      (1994) J.Biol.Chem. 269: 20811


    Organizational Affiliation

    Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE A
A, B
313Streptomyces lividansGene Names: xlnA
EC: 3.2.1.8
Find proteins for P26514 (Streptomyces lividans)
Go to UniProtKB:  P26514
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
X2F
Query on X2F

Download SDF File 
Download CCD File 
A, B
2-DEOXY-2-FLUORO XYLOPYRANOSE
C5 H9 F O4
YVMHSZGJGHRGOD-MBMOQRBOSA-N
 Ligand Interaction
XYP
Query on XYP

Download SDF File 
Download CCD File 
A, B
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.210α = 90.00
b = 81.060β = 102.79
c = 72.810γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-05
    Type: Initial release
  • Version 1.1: 2011-08-31
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance