4C2L

Crystal structure of endo-xylogalacturonan hydrolase from Aspergillus tubingensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Endo-Xylogalacturonan Hydrolase from Aspergillus Tubingensis.

Rozeboom, H.J.Beldman, G.Schols, H.A.Dijkstra, B.W.

(2013) FEBS J 280: 6061

  • DOI: 10.1111/febs.12524
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Endo-xylogalacturonan hydrolase is a member of glycoside hydrolase family 28 (GH28) that hydrolyzes the glycosidic bond between two β-xylose-substituted galacturonic acid residues in pectin. Presented here is the X-ray crystal structure of the endo-x ...

    Endo-xylogalacturonan hydrolase is a member of glycoside hydrolase family 28 (GH28) that hydrolyzes the glycosidic bond between two β-xylose-substituted galacturonic acid residues in pectin. Presented here is the X-ray crystal structure of the endo-xylogalacturonan hydrolase from Aspergillus tubingensis (XghA) at 1.75 Å resolution. The high degree of structural conservation in the active site and catalytic apparatus compared with polygalacturonases indicates that cleavage of the substrate proceeds in essentially the same way as found for the other GH28 enzymes. Molecular modeling of a xylosylated tri-galacturonate in the active site identified the amino acid residues involved in substrate binding. They border a substrate-binding cleft that is much wider than in other polygalacturonases, and can accommodate xylosylated substrates. The most extensive interactions appear to occur at subsite +2, in agreement with the enzyme kinetics results, which showed enhanced activity on substrates with a xylose attached to the galacturonic acid bound at subsite +2.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-XYLOGALACTURONAN HYDROLASE A
A
388Aspergillus tubingensisMutation(s): 0 
Gene Names: xghA
EC: 3.2.1
Find proteins for Q9UUZ2 (Aspergillus tubingensis)
Go to UniProtKB:  Q9UUZ2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.44α = 90
b = 121.18β = 90
c = 129.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-02-27
    Changes: Data collection, Derived calculations, Experimental preparation