4A4A

CpGH89 (E483Q, E601Q), from Clostridium perfringens, in complex with its substrate GlcNAc-alpha-1,4-galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Structural analysis of a bacterial exo-alpha-D-N-acetylglucosaminidase in complex with an unusual disaccharide found in class III mucin.

Ficko-Blean, E.Boraston, A.B.

(2012) Glycobiology 22: 590-595

  • DOI: 10.1093/glycob/cwr165
  • Primary Citation of Related Structures:  
    4A4A

  • PubMed Abstract: 
  • CpGH89 is a family 89 glycoside hydrolase with exo-α-D-N-acetylglucosaminidase activity that is produced by the human and animal pathogen Clostridium perfringens. This enzyme is active on the α-D-GlcpNAc-(1 → 4)-D-Galp motif that is displayed on the class III mucins within the gastric mucosa ...

    CpGH89 is a family 89 glycoside hydrolase with exo-α-D-N-acetylglucosaminidase activity that is produced by the human and animal pathogen Clostridium perfringens. This enzyme is active on the α-D-GlcpNAc-(1 → 4)-D-Galp motif that is displayed on the class III mucins within the gastric mucosa. Other members of this enzyme family, such as human NAGLU, are active on heparan. A truncated version of CpGH89 was rendered inactive through the mutation of two key catalytic residues, the protein crystallized and its structure determined in complex with α-D-GlcpNAc-(1 → 4)-D-Galp to reveal the molecular details of how this unique disaccharide is recognized by CpGH89. An analysis of this substrate complex not only provides insight into how this enzyme selects for its mucin-presented substrate but also advances our understanding of how its clinically relevant mammalian counterparts are specific for heparan.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEINA914Clostridium perfringensMutation(s): 2 
EC: 3.2.1.50
UniProt
Find proteins for Q8XM24 (Clostridium perfringens (strain 13 / Type A))
Explore Q8XM24 
Go to UniProtKB:  Q8XM24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XM24
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranoseB 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G94473FP
GlyCosmos:  G94473FP
GlyGen:  G94473FP
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
N [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.996α = 90
b = 90.996β = 90
c = 252.856γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Database references
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary