2JEN

Family 12 xyloglucanase from Bacillus licheniformis in complex with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 

wwPDB Validation   3D Report Full Report


This is version 2.0 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.S.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:  
    2JEQ, 2JEP, 2JEN, 2JEM

  • 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDO-BETA-1,4-GLUCANASE A261Bacillus licheniformisMutation(s): 1 
Gene Names: 
EC: 3.2.1.4 (PDB Primary Data), 3.2.1.151 (PDB Primary Data)
Find proteins for Q7X4S4 (Bacillus licheniformis)
Explore Q7X4S4 
Go to UniProtKB:  Q7X4S4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
6 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-xylopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]alpha-D-glucopyranose
C
4 N/A Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download Ideal Coordinates CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.629α = 90
b = 114.629β = 90
c = 110.302γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary