2J74

Structure of Beta-1,4-Galactanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Investigating the Binding of Beta-1,4-Galactan to Bacillus Licheniformis Beta-1,4-Galactanase by Crystallography and Computational Modeling.

Le Nours, J.De Maria, L.Welner, D.Jorgensen, C.T.Christensen, L.L.H.Borchert, T.V.Larsen, S.Lo Leggio, L.

(2009) Proteins 75: 977

  • DOI: 10.1002/prot.22310
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microbial beta-1,4-galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH-A of glycosid ...

    Microbial beta-1,4-galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH-A of glycoside hydrolases, which cover many different poly- and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis beta-1,4-galactanase and its inactive nucleophile mutant have been obtained with methyl-beta(1-->4)-galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the beta-1,4-galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a beta(1-->4)-galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite -4 to +5. In particular, this analysis newly identified a conserved beta-turn, which contributes to subsites -2 to +3. This beta-turn is unique to family 53 beta-1,4-galactanases among all clan GH-A families that have been structurally characterized and thus might be a structural signature for endo-beta-1,4-galactanase specificity.


    Organizational Affiliation

    Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YVFO
A, B
399Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)Mutation(s): 0 
Gene Names: ganB (galA, yvfO)
EC: 3.2.1.89
Find proteins for Q65CX5 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46))
Go to UniProtKB:  Q65CX5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
B2G
Query on B2G

Download SDF File 
Download CCD File 
A, B
GALACTOBIOSE
BETA-1,4-GALACTOBIOSIDE
C12 H22 O11
GUBGYTABKSRVRQ-WWZHPTPQSA-N
 Ligand Interaction
B4G
Query on B4G

Download SDF File 
Download CCD File 
A, B
GALACTOTRIOSE
BETA-1,4-GALACTOTRIOSIDE
C18 H32 O16
FYGDTMLNYKFZSV-XJJKTWKOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.430α = 90.00
b = 80.250β = 99.50
c = 104.500γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-18
    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: 2018-01-17
    Type: Data collection