2V72

The structure of the family 32 CBM from C. perfringens NanJ in complex with galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Carbohydrate Recognition by a Large Sialidase Toxin from Clostridium Perfringens.

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

(2007) Biochemistry 46: 11352

  • DOI: 10.1021/bi701317g
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Myonecrotic isolates of Clostridium perfringens secrete multimodular sialidases, often termed "large sialidases", that contribute to the virulence of this bacterium. NanJ is the largest of the two secreted sialidases at 1173 amino acids and comprises ...

    Myonecrotic isolates of Clostridium perfringens secrete multimodular sialidases, often termed "large sialidases", that contribute to the virulence of this bacterium. NanJ is the largest of the two secreted sialidases at 1173 amino acids and comprises 6 different modules which are, from the N-terminus, a family 32 carbohydrate binding module (CBM), a family 40 CBM, a family 33 glycoside hydrolase, a module of unknown function, a family 82 "X-module" of unknown function, and a module with amino acid similarity to fibronectin type III domains. The hydrolase activity of clostridial sialidases is quite well documented; however, the functions of their accessory domains are entirely uninvestigated. Here we describe the carbohydrate binding activity of the isolated family 32 CBM (CBM32) and the isolated family 40 CBM (CBM40). CBM32 is shown to bind galactose or N-acetylgalactosamine, while CBM40 is sialic acid specific, though both CBMs appear to bind with very low affinities. The crystal structure of CBM32 was determined at 2.25 A in complex with galactose. This revealed what appears to be a very simple galactose binding site. The crystal structure of CBM40 was determined at 2.20 A in complex with a sialic acid containing molecule that it fortuitously crystallized with, revealing the molecular details of the CBM40-sialic acid interaction. Overall, the results indicate that NanJ contains carbohydrate specific binding modules that likely function to target the enzyme to molecules or cells bearing mixed populations of glycans that terminate in either galactose/N-acetylgalactosamine or sialic acid.


    Organizational Affiliation

    Biochemistry & Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada. boraston@uvic.ca



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXO-ALPHA-SIALIDASEA143Clostridium perfringensMutation(s): 0 
Find proteins for Q8XMY5 (Clostridium perfringens (strain 13 / Type A))
Explore Q8XMY5 
Go to UniProtKB:  Q8XMY5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download CCD File 
A
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GALKa:  1360   M^-1  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.265α = 90
b = 45.86β = 90
c = 69.003γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary