2JEP

Native family 5 xyloglucanase from Paenibacillus pabuli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization and Three-Dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families Gh5 and Gh12.

Gloster, T.M.Ibatullin, F.M.Macauley, K.Eklof, J.M.Roberts, S.Turkenburg, J.P.Bjornvad, M.E.Jorgensen, P.L.Danielsen, S.Johansen, K.Borchert, T.V.Wilson, K.S.Brumer, H.Davies, G.J.

(2007) J Biol Chem 282: 19177

  • DOI: 10.1074/jbc.M700224200
  • Primary Citation of Related Structures:  
    2JEM, 2JEN, 2JEP, 2JEQ

  • PubMed Abstract: 
  • The plant cell wall is a complex material in which the cellulose microfibrils are embedded within a mesh of other polysaccharides, some of which are loosely termed "hemicellulose." One such hemicellulose is xyloglucan, which displays a beta-1,4-linked d-glucose backbone substituted with xylose, galactose, and occasionally fucose moieties ...

    The plant cell wall is a complex material in which the cellulose microfibrils are embedded within a mesh of other polysaccharides, some of which are loosely termed "hemicellulose." One such hemicellulose is xyloglucan, which displays a beta-1,4-linked d-glucose backbone substituted with xylose, galactose, and occasionally fucose moieties. Both xyloglucan and the enzymes responsible for its modification and degradation are finding increasing prominence, reflecting both the drive for enzymatic biomass conversion, their role in detergent applications, and the utility of modified xyloglucans for cellulose fiber modification. Here we present the enzymatic characterization and three-dimensional structures in ligand-free and xyloglucan-oligosaccharide complexed forms of two distinct xyloglucanases from glycoside hydrolase families GH5 and GH12. The enzymes, Paenibacillus pabuli XG5 and Bacillus licheniformis XG12, both display open active center grooves grafted upon their respective (beta/alpha)(8) and beta-jelly roll folds, in which the side chain decorations of xyloglucan may be accommodated. For the beta-jelly roll enzyme topology of GH12, binding of xylosyl and pendant galactosyl moieties is tolerated, but the enzyme is similarly competent in the degradation of unbranched glucans. In the case of the (beta/alpha)(8) GH5 enzyme, kinetically productive interactions are made with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides. The differential strategies for the accommodation of the side chains of xyloglucan presumably facilitate the action of these microbial hydrolases in milieus where diverse and differently substituted substrates may be encountered.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XYLOGLUCANASEA, B395Paenibacillus pabuliMutation(s): 0 
EC: 3.2.1.151 (PDB Primary Data), 3.2.1.4 (UniProt)
UniProt
Find proteins for H9KVH3 (Paenibacillus pabuli)
Explore H9KVH3 
Go to UniProtKB:  H9KVH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9KVH3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.416α = 90
b = 89.574β = 90
c = 90.397γ = 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: 2007-03-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance