2C71

The structure of a family 4 acetyl xylan esterase from Clostridium thermocellum in complex with a magnesium ion.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and Activity of Two Metal-Ion Dependent Acetyl Xylan Esterases Involved in Plant Cell-Wall Degradation Reveals a Close Similarity to Peptidoglycan Deacetylases.

Taylor, E.J.Gloster, T.M.Turkenburg, P.J.Vincent, F.Brzozowski, A.M.Dupont, C.Shareck, F.Centeno, M.S.J.Prates, J.A.M.Ferreira, L.M.A.Fontes, C.M.G.A.Biely, P.Davies, G.J.

(2006) J.Biol.Chem. 281: 10968

  • DOI: 10.1074/jbc.M513066200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzymatic degradation of plant cell wall xylan requires the concerted action of a diverse enzymatic syndicate. Among these enzymes are xylan esterases, which hydrolyze the O-acetyl substituents, primarily at the O-2 position of the xylan backbone ...

    The enzymatic degradation of plant cell wall xylan requires the concerted action of a diverse enzymatic syndicate. Among these enzymes are xylan esterases, which hydrolyze the O-acetyl substituents, primarily at the O-2 position of the xylan backbone. All acetylxylan esterase structures described previously display a alpha/beta hydrolase fold with a "Ser-His-Asp" catalytic triad. Here we report the structures of two distinct acetylxylan esterases, those from Streptomyces lividans and Clostridium thermocellum, in native and complex forms, with x-ray data to between 1.6 and 1.0 A resolution. We show, using a novel linked assay system with PNP-2-O-acetylxyloside and a beta-xylosidase, that the enzymes are sugar-specific and metal ion-dependent and possess a single metal center with a chemical preference for Co2+. Asp and His side chains complete the catalytic machinery. Different metal ion preferences for the two enzymes may reflect the surprising diversity with which the metal ion coordinates residues and ligands in the active center environment of the S. lividans and C. thermocellum enzymes. These "CE4" esterases involved in plant cell wall degradation are shown to be closely related to the de-N-acetylases involved in chitin and peptidoglycan degradation (Blair, D. E., Schuettelkopf, A. W., MacRae, J. I., and Aalten, D. M. (2005) Proc. Natl. Acad. Sci. U. S. A., 102, 15429-15434), which form the NodB deacetylase "superfamily."


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOSIDE HYDROLASE, FAMILY 11\:CLOSTRIDIUM CELLULOSOME ENZYME, DOCKERIN TYPE I\:POLYSACCHARIDE
A
216Clostridium thermocellumMutation(s): 0 
Gene Names: xynA
EC: 3.2.1.8
Find proteins for O87119 (Clostridium thermocellum)
Go to UniProtKB:  O87119
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.124 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.064α = 90.00
b = 106.064β = 90.00
c = 35.466γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Refinement description