2W1Q

Unique ligand binding specificity for a family 32 Carbohydrate- Binding Module from the Mu toxin produced by Clostridium perfringens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

N-Acetylglucosamine Recognition by a Family 32 Carbohydrate-Binding Module from Clostridium Perfringens Nagh.

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

(2009) J Mol Biol 390: 208

  • DOI: 10.1016/j.jmb.2009.04.066
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many carbohydrate-active enzymes have complex architectures comprising multiple modules that may be involved in catalysis, carbohydrate binding, or protein-protein interactions. Carbohydrate-binding modules (CBMs) are a common ancillary module whose ...

    Many carbohydrate-active enzymes have complex architectures comprising multiple modules that may be involved in catalysis, carbohydrate binding, or protein-protein interactions. Carbohydrate-binding modules (CBMs) are a common ancillary module whose function is to promote the adherence of the complete enzyme to carbohydrate substrates. CBM family 32 has been proposed to be one of the most diverse CBM families classified to date, yet all of the structurally characterized CBM32s thus far recognize galactose-based ligands. Here, we report a unique binding specificity and mode of ligand binding for a family 32 CBM. NagHCBM32-2 is one of four CBM32 modules in NagH, a family 84 glycoside hydrolase secreted by Clostridium perfringens. NagHCBM32-2 has the beta-sandwich scaffold common to members of the family; however, its specificity for N-acetylglucosamine is unusual among CBMs. X-ray crystallographic analysis of the module at resolutions from 1.45 to 2.0 A and in complex with disaccharides reveals that its mode of sugar recognition is quite different from that observed for galactose-specific CBM32s. This study continues to unravel the diversity of CBMs found in family 32 and how these CBMs might impart the carbohydrate-binding specificity to the extracellular glycoside hydrolases in C. perfringens.


    Organizational Affiliation

    University of Victoria, BC, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYALURONOGLUCOSAMINIDASEA, B192Clostridium perfringensMutation(s): 1 
EC: 3.2.1.35
Find proteins for P26831 (Clostridium perfringens (strain 13 / Type A))
Explore P26831 
Go to UniProtKB:  P26831
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download CCD File 
A
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.118α = 90
b = 61.47β = 90
c = 82.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    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: 2019-10-23
    Changes: Advisory, Data collection, Database references, Other