1E0V

Xylanase 10A from Sreptomyces lividans. cellobiosyl-enzyme intermediate at 1.7 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 

Starting Model: experimental
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This is version 2.1 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

  • DOI: https://doi.org/10.1074/jbc.275.30.23020
  • Primary Citation of Related Structures:  
    1E0V, 1E0W, 1E0X

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASE A313Streptomyces lividansMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for P26514 (Streptomyces lividans)
Explore P26514 
Go to UniProtKB:  P26514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26514
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G29564OM
GlyCosmos:  G29564OM
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.87α = 90
b = 46.27β = 90
c = 87.07γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-05
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary