4A6O

CpGH89CBM32-4, produced by Clostridium perfringens, in complex with glcNAc-alpha-1,4-galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.287 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Carbohydrate Recognition by an Architecturally Complex Alpha-N-Acetylglucosaminidase from Clostridium Perfringens.

Ficko-Blean, E.Stuart, C.P.Suits, M.D.Cid, M.Tessier, M.Woods, R.J.Boraston, A.B.

(2012) PLoS One 7: 33524

  • DOI: https://doi.org/10.1371/journal.pone.0033524
  • Primary Citation of Related Structures:  
    4A3Z, 4A41, 4A42, 4A44, 4A45, 4A6O, 4AAX

  • PubMed Abstract: 

    CpGH89 is a large multimodular enzyme produced by the human and animal pathogen Clostridium perfringens. The catalytic activity of this exo-α-D-N-acetylglucosaminidase is directed towards a rare carbohydrate motif, N-acetyl-β-D-glucosamine-α-1,4-D-galactose, which is displayed on the class III mucins deep within the gastric mucosa. In addition to the family 89 glycoside hydrolase catalytic module this enzyme has six modules that share sequence similarity to the family 32 carbohydrate-binding modules (CBM32s), suggesting the enzyme has considerable capacity to adhere to carbohydrates. Here we suggest that two of the modules, CBM32-1 and CBM32-6, are not functional as carbohydrate-binding modules (CBMs) and demonstrate that three of the CBMs, CBM32-3, CBM32-4, and CBM32-5, are indeed capable of binding carbohydrates. CBM32-3 and CBM32-4 have a novel binding specificity for N-acetyl-β-D-glucosamine-α-1,4-D-galactose, which thus complements the specificity of the catalytic module. The X-ray crystal structure of CBM32-4 in complex with this disaccharide reveals a mode of recognition that is based primarily on accommodation of the unique bent shape of this sugar. In contrast, as revealed by a series of X-ray crystal structures and quantitative binding studies, CBM32-5 displays the structural and functional features of galactose binding that is commonly associated with CBM family 32. The functional CBM32s that CpGH89 contains suggest the possibility for multivalent binding events and the partitioning of this enzyme to highly specific regions within the gastrointestinal tract.


  • Organizational Affiliation

    Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
A, B
161Clostridium perfringensMutation(s): 0 
EC: 3.2.1.50
UniProt
Find proteins for A0A0H2YU91 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore A0A0H2YU91 
Go to UniProtKB:  A0A0H2YU91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2YU91
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan:  G94473FP
GlyCosmos:  G94473FP
GlyGen:  G94473FP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.287 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.71α = 90
b = 49.89β = 90
c = 63.17γ = 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: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Other
  • Version 1.2: 2013-07-24
    Changes: Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Structure summary