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


Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1111/febs.12524
  • Primary Citation of Related Structures:  
    4C2L

  • 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-xylogalacturonan hydrolase from Aspergillus tubingensis (XghA) at 1 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDO-XYLOGALACTURONAN HYDROLASE AA388Aspergillus tubingensisMutation(s): 0 
Gene Names: xghA
EC: 3.2.1
UniProt
Find proteins for Q9UUZ2 (Aspergillus tubingensis)
Explore Q9UUZ2 
Go to UniProtKB:  Q9UUZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUZ2
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
MAN
Query on MAN
Download Ideal Coordinates CCD File 
C [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
L [auth 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



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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