2V5D

Structure of a Family 84 Glycoside Hydrolase and a Family 32 Carbohydrate-Binding Module in Tandem from Clostridium perfringens.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.325 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Portrait of an Enzyme: A Complete Structural Analysis of a Multi-Modular Beta-N-Acetylglucosaminidase from Clostridium Perfringens

Ficko-Blean, E.Gregg, K.J.Adams, J.J.Hehemann, J.H.Smith, S.J.Czjzek, M.Boraston, A.B.

(2009) J Biol Chem 284: 9876

  • DOI: 10.1074/jbc.M808954200
  • Primary Citation of Related Structures:  
    2V5C, 2V5D, 2W1N

  • PubMed Abstract: 
  • Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging ...

    Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens micro-toxin, which was determined using a combination of small angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.


    Organizational Affiliation

    Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-GLCNACASE NAGJA737Clostridium perfringensMutation(s): 0 
EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
UniProt
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore Q0TR53 
Go to UniProtKB:  Q0TR53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0TR53
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.325 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.851α = 90
b = 69.546β = 95.78
c = 136.78γ = 90
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: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance